chr3-130441090-G-T

Variant names:

• chr3-130441090-G-T
• rs7629719
• NM_001278298.2:c.6487+265G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278298.2(COL6A5):​c.6487+265G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,114 control chromosomes in the GnomAD database, including 60,681 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 0.89 (60681 hom., cov: 31)
• Consequence: COL6A5 NM_001278298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278298.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL6A5	NM_001278298.2	MANE Select	c.6487+265G>T		intron	N/A	NP_001265227.1
	COL6A5	NM_153264.7		c.6487+265G>T		intron	N/A	NP_694996.5
	COL6A5	NR_022012.3		n.6825+265G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL6A5	ENST00000373157.9	TSL:2 MANE Select	c.6487+265G>T		intron	N/A	ENSP00000362250.5
	COL6A5	ENST00000312481.11	TSL:1	n.6487+265G>T		intron	N/A	ENSP00000309762.7
	COL6A5	ENST00000512836.6	TSL:2	c.6487+265G>T		intron	N/A	ENSP00000422898.2

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135370 AN: 151996 Hom.: 60657 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.884

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.890 AC: 135452 AN: 152114 Hom.: 60681 Cov.: 31 AF XY: 0.893 AC XY: 66395 AN XY: 74378

African (AFR) AF: 0.785 AC: 32552 AN: 41472

American (AMR) AF: 0.917 AC: 13995 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3113 AN: 3472

East Asian (EAS) AF: 0.838 AC: 4330 AN: 5164

South Asian (SAS) AF: 0.853 AC: 4110 AN: 4816

European-Finnish (FIN) AF: 0.979 AC: 10386 AN: 10612

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.941 AC: 63999 AN: 68000

Other (OTH) AF: 0.884 AC: 1866 AN: 2112

Alfa AF: 0.924 Hom.: 28771

Bravo AF: 0.882

Asia WGS AF: 0.836 AC: 2908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.5
DANN	Benign	0.52
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7629719; hg19: chr3-130159934;