14-80191639-T-C

Variant names:

• chr14-80191639-T-C
• rs225022

Variant summary

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

The variant allele was found at a frequency of 0.484 in 151,812 control chromosomes in the GnomAD database, including 18,245 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 0.48 (18245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73450 AN: 151694 Hom.: 18226 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.484 AC: 73507 AN: 151812 Hom.: 18245 Cov.: 32 AF XY: 0.485 AC XY: 36003 AN XY: 74200

African (AFR) AF: 0.520 AC: 21514 AN: 41360

American (AMR) AF: 0.525 AC: 8026 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3816 AN: 5158

South Asian (SAS) AF: 0.551 AC: 2646 AN: 4804

European-Finnish (FIN) AF: 0.388 AC: 4076 AN: 10518

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30171 AN: 67912

Other (OTH) AF: 0.481 AC: 1013 AN: 2108

Alfa AF: 0.439 Hom.: 1852

Bravo AF: 0.497

Asia WGS AF: 0.657 AC: 2280 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs225022; hg19: chr14-80657982;