rs10087151

Variant names:

• chr8-120160022-G-A
• rs10087151
• NM_021110.4:c.205+1776G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-120160022-G-A
• chr8-120160022-G-T

Variant summary

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

The NM_021110.4(COL14A1):​c.205+1776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,132 control chromosomes in the GnomAD database, including 52,466 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 0.83 (52466 hom., cov: 31)
• Consequence: COL14A1 NM_021110.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 5 publications found

Genes affected

COL14A1 (HGNC:2191): (collagen type XIV alpha 1 chain) This gene encodes the alpha chain of type XIV collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XIV collagen interacts with the fibril surface and is involved in the regulation of fibrillogenesis. [provided by RefSeq, Jan 2013]

COL14A1 Gene-Disease associations (from GenCC):

• punctate palmoplantar keratoderma type 1

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary palmoplantar keratoderma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL14A1	NM_021110.4	c.205+1776G>A		intron_variant	Intron 3 of 47	ENST00000297848.8	NP_066933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL14A1	ENST00000297848.8	c.205+1776G>A		intron_variant	Intron 3 of 47	5	NM_021110.4	ENSP00000297848.3

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125631 AN: 152010 Hom.: 52417 Cov.: 31

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.826 AC: 125735 AN: 152132 Hom.: 52466 Cov.: 31 AF XY: 0.826 AC XY: 61411 AN XY: 74352

African (AFR) AF: 0.948 AC: 39366 AN: 41542

American (AMR) AF: 0.832 AC: 12712 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2870 AN: 3466

East Asian (EAS) AF: 0.759 AC: 3916 AN: 5160

South Asian (SAS) AF: 0.714 AC: 3437 AN: 4814

European-Finnish (FIN) AF: 0.797 AC: 8422 AN: 10568

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52313 AN: 67992

Other (OTH) AF: 0.812 AC: 1713 AN: 2110

Alfa AF: 0.787 Hom.: 25562

Bravo AF: 0.839

Asia WGS AF: 0.693 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.066
DANN	Benign	0.58
PhyloP100		-1.3
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: rs10087151; hg19: chr8-121172261;