3-22939785-G-A

Variant names:

• chr3-22939785-G-A
• rs711702

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 0.0861 in 152,092 control chromosomes in the GnomAD database, including 653 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 0.086 (653 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0863 AC: 13108 AN: 151972 Hom.: 655 Cov.: 32

Gnomad AFR AF: 0.0305

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0852

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0861 AC: 13100 AN: 152092 Hom.: 653 Cov.: 32 AF XY: 0.0856 AC XY: 6365 AN XY: 74360

African (AFR) AF: 0.0304 AC: 1261 AN: 41494

American (AMR) AF: 0.0908 AC: 1386 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3464

East Asian (EAS) AF: 0.0765 AC: 397 AN: 5188

South Asian (SAS) AF: 0.127 AC: 609 AN: 4802

European-Finnish (FIN) AF: 0.0852 AC: 902 AN: 10588

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7525 AN: 67968

Other (OTH) AF: 0.105 AC: 222 AN: 2112

Alfa AF: 0.0760 Hom.: 245

Bravo AF: 0.0829

Asia WGS AF: 0.112 AC: 389 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.15
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs711702; hg19: chr3-22981276;