3-130394792-T-A

Variant names:

• chr3-130394792-T-A
• rs10934938
• NM_001278298.2:c.2993-98T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001278298.2(COL6A5):​c.2993-98T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000153 in 655,372 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: COL6A5 NM_001278298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL6A5	NM_001278298.2	MANE Select	c.2993-98T>A		intron	N/A	NP_001265227.1	H0Y393
	COL6A5	NM_153264.7		c.2993-98T>A		intron	N/A	NP_694996.5
	COL6A5	NR_022012.3		n.3331-98T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL6A5	ENST00000373157.9	TSL:2 MANE Select	c.2993-98T>A		intron	N/A	ENSP00000362250.5	H0Y393
	COL6A5	ENST00000312481.11	TSL:1	n.2993-98T>A		intron	N/A	ENSP00000309762.7	A8TX70-1
	COL6A5	ENST00000512836.6	TSL:2	c.2993-98T>A		intron	N/A	ENSP00000422898.2	A8TX70-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000153 AC: 1 AN: 655372 Hom.: 0 AF XY: 0.00000293 AC XY: 1 AN XY: 341030

African (AFR) AF: 0.00 AC: 0 AN: 15980

American (AMR) AF: 0.00 AC: 0 AN: 19550

Ashkenazi Jewish (ASJ) AF: 0.0000570 AC: 1 AN: 17532

East Asian (EAS) AF: 0.00 AC: 0 AN: 31932

South Asian (SAS) AF: 0.00 AC: 0 AN: 52564

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34396

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2498

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 447870

Other (OTH) AF: 0.00 AC: 0 AN: 33050

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.86
PhyloP100		-0.40

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: rs10934938; hg19: chr3-130113635;