rs10104973

Variant names:

• chr8-120092146-G-A
• rs10104973
• ENST00000498051.6:n.-134-13437G>A

Variant summary

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

The ENST00000498051.6(COL14A1):​n.-134-13437G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 151,928 control chromosomes in the GnomAD database, including 45,506 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 0.77 (45506 hom., cov: 29)
• Consequence: COL14A1 ENST00000498051.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• 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

LOC105375730 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375730	XR_928593.4	n.1422-13437G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL14A1	ENST00000498051.6	n.-134-13437G>A		intron_variant	Intron 2 of 22	1		ENSP00000428851.1

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117459 AN: 151810 Hom.: 45497 Cov.: 29

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.774 AC: 117521 AN: 151928 Hom.: 45506 Cov.: 29 AF XY: 0.775 AC XY: 57534 AN XY: 74248

African (AFR) AF: 0.768 AC: 31821 AN: 41426

American (AMR) AF: 0.807 AC: 12319 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2825 AN: 3470

East Asian (EAS) AF: 0.749 AC: 3857 AN: 5150

South Asian (SAS) AF: 0.720 AC: 3448 AN: 4788

European-Finnish (FIN) AF: 0.797 AC: 8415 AN: 10560

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.769 AC: 52226 AN: 67958

Other (OTH) AF: 0.774 AC: 1636 AN: 2114

Alfa AF: 0.775 Hom.: 132922

Bravo AF: 0.779

Asia WGS AF: 0.689 AC: 2398 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	0.28
DANN	Benign	0.39
PhyloP100		-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10104973; hg19: chr8-121104385;