1-31691408-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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

GnomAD3 exomes AF: 0.193 AC: 46904 AN: 243274 Hom.: 5897 AF XY: 0.196 AC XY: 25902 AN XY: 132012

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 SAS exome AF: 0.386

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

Gnomad4 AFR exome AF: 0.118

Gnomad4 AMR exome AF: 0.326

Gnomad4 ASJ exome AF: 0.110

Gnomad4 EAS exome AF: 0.163

Gnomad4 SAS exome AF: 0.379

Gnomad4 FIN exome AF: 0.185

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.145

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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.134

Alfa AF: 0.137 Hom.: 1181

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2297679; hg19: chr1-32157009; COSMIC: COSV54716463; COSMIC: COSV54716463;