NM_001848.3(COL6A1):c.996C>T (p.Gly332=) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Oct 1, 2022
Review status:: criteria provided, conflicting classifications

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000725117.22

Allele description [Variation Report for NM_001848.3(COL6A1):c.996C>T (p.Gly332=)]

NM_001848.3(COL6A1):c.996C>T (p.Gly332=)

Gene:

COL6A1:collagen type VI alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_001848.3(COL6A1):c.996C>T (p.Gly332=)

HGVS:

NC_000021.9:g.45990416C>T
NG_008674.1:g.13668C>T
NM_001848.3:c.996C>TMANE SELECT
NP_001839.2:p.Gly332=
NP_001839.2:p.Gly332=
LRG_475t1:c.996C>T
LRG_475:g.13668C>T
LRG_475p1:p.Gly332=
NC_000021.8:g.47410330C>T
NM_001848.2:c.996C>T

Links:

dbSNP: rs11702055

NCBI 1000 Genomes Browser:

rs11702055

Molecular consequence:

NM_001848.3:c.996C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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MULTISPECIES: TraY domain-containing protein [Klebsiella]
MULTISPECIES: TraY domain-containing protein [Klebsiella]
gi|1846582296|ref|WP_171972759.1|

Protein
MULTISPECIES: ISNCY family transposase [Klebsiella]
MULTISPECIES: ISNCY family transposase [Klebsiella]
gi|1148478788|ref|WP_077266289.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000334228	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Oct 10, 2017)	germline	clinical testing	Citation Link,
SCV000680650	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Dec 8, 2017)	germline	clinical testing	Citation Link,
SCV002821096	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Oct 1, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000334228

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Oct 10, 2017)

germline

clinical testing

Citation Link,

SCV000680650

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Dec 8, 2017)

germline

clinical testing

Citation Link,

SCV002821096

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Oct 1, 2022)

germline

clinical testing

Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	5	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000334228.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		5	not provided	not provided	not provided

From GeneDx, SCV000680650.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.996 C>T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.996 C>T variant is observed in 18/23704 (0.1%) alleles from individuals of Latino background, in large population cohorts (Lek et al., 2016). Several splice prediction algorithms are inconsistent in their predictions as to whether or not the c.996C>T alteration damages the natural donor site in intron 13 or introduces a cryptic donor site in exon 13. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV002821096.14

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

Description

COL6A1: BP4, BP7

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		2	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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