1-31691408-G-T

Variant names:

• chr1-31691408-G-T
• rs2297679
• NM_001856.4:c.1398+9C>A

Variant summary

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

The NM_001856.4(COL16A1):​c.1398+9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,606,712 control chromosomes in the GnomAD database, including 21,793 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 0.15 (2026 hom., cov: 33)
  • Exomes 𝑓: 0.15 (19767 hom.)
• Consequence: COL16A1 NM_001856.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 7 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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL16A1	NM_001856.4	c.1398+9C>A		intron_variant	Intron 19 of 70	ENST00000373672.8	NP_001847.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL16A1	ENST00000373672.8	c.1398+9C>A		intron_variant	Intron 19 of 70	5	NM_001856.4	ENSP00000362776.3
COL16A1	ENST00000373668.7	c.1398+9C>A		intron_variant	Intron 19 of 40	2		ENSP00000362772.3
COL16A1	ENST00000373667.4	c.555+9C>A		intron_variant	Intron 11 of 16	5		ENSP00000362771.4

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22443 AN: 152028 Hom.: 2012 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.136

GnomAD2 exomes AF: 0.193 AC: 46904 AN: 243274 AF XY: 0.196

Gnomad AFR exome AF: 0.117

Gnomad AMR exome AF: 0.331

Gnomad ASJ exome AF: 0.104

Gnomad EAS exome AF: 0.153

Gnomad FIN exome AF: 0.186

Gnomad NFE exome AF: 0.126

Gnomad OTH exome AF: 0.165

GnomAD4 exome AF: 0.148 AC: 215884 AN: 1454566 Hom.: 19767 Cov.: 39 AF XY: 0.155 AC XY: 111888 AN XY: 722896

African (AFR) AF: 0.118 AC: 3932 AN: 33278

American (AMR) AF: 0.326 AC: 14347 AN: 43996

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 2806 AN: 25504

East Asian (EAS) AF: 0.163 AC: 6454 AN: 39588

South Asian (SAS) AF: 0.379 AC: 32355 AN: 85478

European-Finnish (FIN) AF: 0.185 AC: 9842 AN: 53098

Middle Eastern (MID) AF: 0.0980 AC: 561 AN: 5722

European-Non Finnish (NFE) AF: 0.124 AC: 136915 AN: 1107908

Other (OTH) AF: 0.145 AC: 8672 AN: 59994

GnomAD4 genome AF: 0.148 AC: 22479 AN: 152146 Hom.: 2026 Cov.: 33 AF XY: 0.156 AC XY: 11573 AN XY: 74396

African (AFR) AF: 0.114 AC: 4738 AN: 41526

American (AMR) AF: 0.244 AC: 3726 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3466

East Asian (EAS) AF: 0.157 AC: 813 AN: 5166

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4822

European-Finnish (FIN) AF: 0.192 AC: 2035 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8506 AN: 67946

Other (OTH) AF: 0.134 AC: 283 AN: 2110

Alfa AF: 0.137 Hom.: 1429

Bravo AF: 0.146

Asia WGS AF: 0.278 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.8
DANN	Benign	0.67
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2297679; hg19: chr1-32157009; COSMIC: COSV54716463; COSMIC: COSV54716463;