rs7643223

Variant names:

• chr3-164008445-T-G
• rs7643223

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 0.58 in 151,942 control chromosomes in the GnomAD database, including 26,391 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 0.58 (26391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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: 0.580 AC: 88036 AN: 151826 Hom.: 26340 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.580 AC: 88147 AN: 151942 Hom.: 26391 Cov.: 32 AF XY: 0.580 AC XY: 43064 AN XY: 74260

African (AFR) AF: 0.735 AC: 30453 AN: 41420

American (AMR) AF: 0.530 AC: 8093 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2059 AN: 3464

East Asian (EAS) AF: 0.617 AC: 3179 AN: 5152

South Asian (SAS) AF: 0.493 AC: 2377 AN: 4818

European-Finnish (FIN) AF: 0.506 AC: 5346 AN: 10556

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34468 AN: 67940

Other (OTH) AF: 0.614 AC: 1295 AN: 2110

Alfa AF: 0.551 Hom.: 4110

Bravo AF: 0.589

Asia WGS AF: 0.590 AC: 2051 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.69
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7643223; hg19: chr3-163726233;