rs434713

Variant names:

• chr14-56075316-A-G
• rs434713

Your query was ambiguous. Multiple possible variants found:

• chr14-56075316-A-G
• chr14-56075316-A-T

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 0.157 in 152,128 control chromosomes in the GnomAD database, including 2,179 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 0.16 (2179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 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: 0.157 AC: 23857 AN: 152010 Hom.: 2171 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0596

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.157 AC: 23891 AN: 152128 Hom.: 2179 Cov.: 32 AF XY: 0.160 AC XY: 11871 AN XY: 74380

African (AFR) AF: 0.228 AC: 9445 AN: 41480

American (AMR) AF: 0.130 AC: 1984 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0596 AC: 207 AN: 3472

East Asian (EAS) AF: 0.325 AC: 1676 AN: 5160

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4816

European-Finnish (FIN) AF: 0.111 AC: 1179 AN: 10592

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7728 AN: 68010

Other (OTH) AF: 0.127 AC: 269 AN: 2110

Alfa AF: 0.127 Hom.: 2009

Bravo AF: 0.158

Asia WGS AF: 0.289 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.016
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs434713; hg19: chr14-56542034; COSMIC: COSV68586078;