14-95959443-G-A

Variant names:

• chr14-95959443-G-A
• rs1122359

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 0.123 in 151,992 control chromosomes in the GnomAD database, including 1,430 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 0.12 (1430 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• 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 = 0.201 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: 0.123 AC: 18697 AN: 151874 Hom.: 1430 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.123 AC: 18698 AN: 151992 Hom.: 1430 Cov.: 32 AF XY: 0.125 AC XY: 9265 AN XY: 74290

African (AFR) AF: 0.0274 AC: 1135 AN: 41464

American (AMR) AF: 0.160 AC: 2442 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1093 AN: 5168

South Asian (SAS) AF: 0.111 AC: 532 AN: 4796

European-Finnish (FIN) AF: 0.170 AC: 1791 AN: 10560

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10491 AN: 67962

Other (OTH) AF: 0.139 AC: 292 AN: 2102

Alfa AF: 0.148 Hom.: 1888

Bravo AF: 0.121

Asia WGS AF: 0.167 AC: 579 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	1.6
DANN	Benign	0.26
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1122359; hg19: chr14-96425780; COSMIC: COSV107181235;