rs7643223

Variant names:

• chr3-164008445-T-G
• rs7643223

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 0.58 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.614

Alfa AF: 0.545 Hom.: 3907

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7643223; hg19: chr3-163726233;