14-80191639-T-C

Position:

• chr14-80191639-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.481

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225022; hg19: chr14-80657982;