14-82802362-A-C

Variant names:

• chr14-82802362-A-C
• rs1964413

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 0.662 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
• Publications: 2 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 = 0.913 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: 0.662 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

African (AFR) AF: 0.870 AC: 36070 AN: 41436

American (AMR) AF: 0.713 AC: 10882 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3468

East Asian (EAS) AF: 0.935 AC: 4811 AN: 5144

South Asian (SAS) AF: 0.694 AC: 3346 AN: 4820

European-Finnish (FIN) AF: 0.473 AC: 4983 AN: 10546

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36469 AN: 67922

Other (OTH) AF: 0.629 AC: 1324 AN: 2106

Alfa AF: 0.514 Hom.: 3200

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1964413; hg19: chr14-83268706; COSMIC: COSV70041948;