rs7429763

Variant names:

• chr3-22573151-C-A
• rs7429763

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 0.0697 in 152,162 control chromosomes in the GnomAD database, including 422 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 0.070 (422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.083 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: 0.0698 AC: 10611 AN: 152044 Hom.: 423 Cov.: 32

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.0538

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0614

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

GnomAD4 genome AF: 0.0697 AC: 10610 AN: 152162 Hom.: 422 Cov.: 32 AF XY: 0.0709 AC XY: 5277 AN XY: 74386

African (AFR) AF: 0.0854 AC: 3545 AN: 41518

American (AMR) AF: 0.0825 AC: 1261 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3470

East Asian (EAS) AF: 0.0334 AC: 173 AN: 5184

South Asian (SAS) AF: 0.0885 AC: 426 AN: 4814

European-Finnish (FIN) AF: 0.0538 AC: 569 AN: 10576

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0639 AC: 4348 AN: 68002

Other (OTH) AF: 0.0607 AC: 128 AN: 2108

Alfa AF: 0.0614 Hom.: 369

Bravo AF: 0.0690

Asia WGS AF: 0.0640 AC: 221 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.43
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs7429763; hg19: chr3-22614642;