rs7643438

Variant names:

• chr3-180266069-G-A
• rs7643438

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 0.337 in 151,844 control chromosomes in the GnomAD database, including 8,953 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 0.34 (8953 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51177 AN: 151724 Hom.: 8937 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.337 AC: 51243 AN: 151844 Hom.: 8953 Cov.: 31 AF XY: 0.342 AC XY: 25376 AN XY: 74188

African (AFR) AF: 0.413 AC: 17098 AN: 41392

American (AMR) AF: 0.399 AC: 6084 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 825 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1908 AN: 5154

South Asian (SAS) AF: 0.480 AC: 2311 AN: 4810

European-Finnish (FIN) AF: 0.271 AC: 2856 AN: 10546

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18984 AN: 67910

Other (OTH) AF: 0.342 AC: 722 AN: 2114

Alfa AF: 0.303 Hom.: 12036

Bravo AF: 0.347

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs7643438; hg19: chr3-179983857;