rs1964413

chr14-82802362-A-Cchr14-82802362-A-T

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 0.662 in 151,898 control chromosomes in the GnomAD database, including 35,327 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 0.66 (35327 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

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 = 0.913 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: 0.662 AC: 100509 AN: 151780 Hom.: 35272 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.662 AC: 100624 AN: 151898 Hom.: 35327 Cov.: 31 AF XY: 0.665 AC XY: 49354 AN XY: 74236

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.629

Alfa AF: 0.500 Hom.: 2897

Bravo AF: 0.688

Asia WGS AF: 0.795 AC: 2760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.35
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: rs1964413; hg19: chr14-83268706; COSMIC: COSV70041948;