8-120092146-G-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498051.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL14A1	ENST00000498051.6	TSL:1	n.-134-13437G>A		intron	N/A	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 v4.9

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;