rs7642134

Variant names:

• chr3-86867732-A-G
• rs7642134

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 0.555 in 151,748 control chromosomes in the GnomAD database, including 23,902 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 0.55 (23902 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 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: 0.555 AC: 84131 AN: 151630 Hom.: 23898 Cov.: 30

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.555 AC: 84159 AN: 151748 Hom.: 23902 Cov.: 30 AF XY: 0.555 AC XY: 41115 AN XY: 74134

African (AFR) AF: 0.457 AC: 18934 AN: 41400

American (AMR) AF: 0.475 AC: 7228 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2439 AN: 3466

East Asian (EAS) AF: 0.461 AC: 2358 AN: 5114

South Asian (SAS) AF: 0.602 AC: 2897 AN: 4814

European-Finnish (FIN) AF: 0.641 AC: 6756 AN: 10532

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41606 AN: 67892

Other (OTH) AF: 0.546 AC: 1152 AN: 2108

Alfa AF: 0.599 Hom.: 115099

Bravo AF: 0.536

Asia WGS AF: 0.484 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7642134; hg19: chr3-86916882;