rs5852593

Variant names:

• chr3-130378802-C-CT
• rs5852593
• NM_001278298.2:c.668-615dupT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001278298.2(COL6A5):​c.668-615dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,010 control chromosomes in the GnomAD database, including 7,152 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (7152 hom., cov: 21)
• Consequence: COL6A5 NM_001278298.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 1 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL6A5	NM_001278298.2	c.668-615dupT		intron_variant	Intron 3 of 40	ENST00000373157.9	NP_001265227.1
COL6A5	NM_153264.7	c.668-615dupT		intron_variant	Intron 3 of 39		NP_694996.5
COL6A5	NR_022012.3	n.1006-615dupT		intron_variant	Intron 3 of 41

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL6A5	ENST00000373157.9	c.668-616_668-615insT		intron_variant	Intron 3 of 40	2	NM_001278298.2	ENSP00000362250.5
COL6A5	ENST00000312481.11	n.668-616_668-615insT		intron_variant	Intron 3 of 41	1		ENSP00000309762.7
COL6A5	ENST00000512836.6	c.668-616_668-615insT		intron_variant	Intron 3 of 39	2		ENSP00000422898.2

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43453 AN: 151894 Hom.: 7121 Cov.: 21

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.286 AC: 43539 AN: 152010 Hom.: 7152 Cov.: 21 AF XY: 0.287 AC XY: 21321 AN XY: 74324

African (AFR) AF: 0.397 AC: 16439 AN: 41426

American (AMR) AF: 0.366 AC: 5597 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3472

East Asian (EAS) AF: 0.495 AC: 2544 AN: 5138

South Asian (SAS) AF: 0.307 AC: 1482 AN: 4830

European-Finnish (FIN) AF: 0.139 AC: 1473 AN: 10600

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14244 AN: 67954

Other (OTH) AF: 0.294 AC: 621 AN: 2112

Alfa AF: 0.247 Hom.: 640

Bravo AF: 0.310

Asia WGS AF: 0.438 AC: 1520 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.028
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: rs5852593; hg19: chr3-130097645;