rs10914464

Variant names:

• chr1-31666718-G-A
• rs10914464
• NM_001856.4:c.3358-637C>T

Variant summary

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

The NM_001856.4(COL16A1):​c.3358-637C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,712 control chromosomes in the GnomAD database, including 19,555 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 0.47 (19555 hom., cov: 30)
• Consequence: COL16A1 NM_001856.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 3 publications found

Genes affected

COL16A1 (HGNC:2193): (collagen type XVI alpha 1 chain) This gene encodes the alpha chain of type XVI collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Members of this collagen family are found in association with fibril-forming collagens such as type I and II, and serve to maintain the integrity of the extracellular matrix. High levels of type XVI collagen have been found in fibroblasts and keratinocytes, and in smooth muscle and amnion. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL16A1	NM_001856.4	c.3358-637C>T		intron_variant	Intron 52 of 70	ENST00000373672.8	NP_001847.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL16A1	ENST00000373672.8	c.3358-637C>T		intron_variant	Intron 52 of 70	5	NM_001856.4	ENSP00000362776.3
COL16A1	ENST00000468459.5	n.576-637C>T		intron_variant	Intron 8 of 8	5
COL16A1	ENST00000488128.6	n.955-637C>T		intron_variant	Intron 4 of 22	5

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71010 AN: 151594 Hom.: 19550 Cov.: 30

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.468 AC: 71019 AN: 151712 Hom.: 19555 Cov.: 30 AF XY: 0.469 AC XY: 34742 AN XY: 74100

African (AFR) AF: 0.181 AC: 7487 AN: 41388

American (AMR) AF: 0.498 AC: 7595 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2066 AN: 3458

East Asian (EAS) AF: 0.218 AC: 1124 AN: 5160

South Asian (SAS) AF: 0.601 AC: 2866 AN: 4772

European-Finnish (FIN) AF: 0.615 AC: 6477 AN: 10530

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41700 AN: 67844

Other (OTH) AF: 0.492 AC: 1041 AN: 2114

Alfa AF: 0.551 Hom.: 32270

Bravo AF: 0.448

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.7
DANN	Benign	0.24
PhyloP100		0.013
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: rs10914464; hg19: chr1-32132319;