rs7696472

Variant names:

• chr4-68672462-G-A
• rs7696472

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 0.531 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.608 AC: 25172 AN: 41414

American (AMR) AF: 0.583 AC: 8900 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1572 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2876 AN: 5126

South Asian (SAS) AF: 0.450 AC: 2169 AN: 4816

European-Finnish (FIN) AF: 0.554 AC: 5846 AN: 10550

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32401 AN: 67940

Other (OTH) AF: 0.533 AC: 1120 AN: 2102

Alfa AF: 0.526 Hom.: 10448

Bravo AF: 0.537

Asia WGS AF: 0.480 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7696472; hg19: chr4-69538180;