rs7696472

Variant names:

• chr4-68672462-G-A
• rs7696472

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 0.531 in 151,898 control chromosomes in the GnomAD database, including 21,819 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 0.53 (21819 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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: 0.531 AC: 80531 AN: 151780 Hom.: 21775 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.531 AC: 80633 AN: 151898 Hom.: 21819 Cov.: 31 AF XY: 0.534 AC XY: 39632 AN XY: 74214

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.533

Alfa AF: 0.522 Hom.: 5442

Bravo AF: 0.537

Asia WGS AF: 0.480 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7696472; hg19: chr4-69538180;