Variant 3-130406145-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001278298.2(COL6A5):c.4395C>T(p.Asp1465=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 1,547,310 control chromosomes in the GnomAD database, including 362,653 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.58 ( 28131 hom., cov: 32)

Exomes 𝑓: 0.68 ( 334522 hom. )

Consequence

COL6A5
NM_001278298.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -7.23

Variant links:

Genes affected

COL6A5 (HGNC:26674): (collagen type VI alpha 5 chain) This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

COL6A5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP7

Synonymous conserved (PhyloP=-7.23 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
COL6A5	NM_001278298.2 linkuse as main transcript	c.4395C>T	p.Asp1465=	synonymous_variant	16/41	ENST00000373157.9	NP_001265227.1
COL6A5	NM_153264.7 linkuse as main transcript	c.4395C>T	p.Asp1465=	synonymous_variant	16/40		NP_694996.5
COL6A5	NR_022012.3 linkuse as main transcript	n.4733C>T		non_coding_transcript_exon_variant	16/42

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL6A5	ENST00000373157.9 linkuse as main transcript	c.4395C>T	p.Asp1465=	synonymous_variant	16/41	2	NM_001278298.2	ENSP00000362250	P2
COL6A5	ENST00000312481.11 linkuse as main transcript	c.4395C>T	p.Asp1465=	synonymous_variant, NMD_transcript_variant	16/42	1		ENSP00000309762		A8TX70-1
COL6A5	ENST00000512836.6 linkuse as main transcript	c.4395C>T	p.Asp1465=	synonymous_variant	16/40	2		ENSP00000422898	A2	A8TX70-2

Frequencies

GnomAD3 genomes

AF:

0.579

AC:

87895

AN:

151926

Hom.:

28131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.719

Gnomad AMR

AF:

0.548

Gnomad ASJ

AF:

0.664

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.460

Gnomad FIN

AF:

0.780

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.728

Gnomad OTH

AF:

0.593

GnomAD3 exomes

AF:

0.591

AC:

90933

AN:

153976

Hom.:

29389

AF XY:

0.592

AC XY:

48345

AN XY:

81696

show subpopulations

Gnomad AFR exome

AF:

0.339

Gnomad AMR exome

AF:

0.494

Gnomad ASJ exome

AF:

0.666

Gnomad EAS exome

AF:

0.171

Gnomad SAS exome

AF:

0.479

Gnomad FIN exome

AF:

0.775

Gnomad NFE exome

AF:

0.723

Gnomad OTH exome

AF:

0.628

GnomAD4 exome

AF:

0.680

AC:

949084

AN:

1395264

Hom.:

334522

Cov.:

AF XY:

0.677

AC XY:

465912

AN XY:

688312

show subpopulations

Gnomad4 AFR exome

AF:

0.335

Gnomad4 AMR exome

AF:

0.494

Gnomad4 ASJ exome

AF:

0.675

Gnomad4 EAS exome

AF:

0.164

Gnomad4 SAS exome

AF:

0.482

Gnomad4 FIN exome

AF:

0.769

Gnomad4 NFE exome

AF:

0.727

Gnomad4 OTH exome

AF:

0.632

GnomAD4 genome

AF:

0.578

AC:

87911

AN:

152046

Hom.:

28131

Cov.:

AF XY:

0.575

AC XY:

42763

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.344

Gnomad4 AMR

AF:

0.548

Gnomad4 ASJ

AF:

0.664

Gnomad4 EAS

AF:

0.183

Gnomad4 SAS

AF:

0.460

Gnomad4 FIN

AF:

0.780

Gnomad4 NFE

AF:

0.728

Gnomad4 OTH

AF:

0.585

Alfa

AF:

0.654

Hom.:

22042

Bravo

AF:

0.548

Asia WGS

AF:

0.316

AC:

1101

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.050

DANN

Benign

0.32

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over