3-22432238-A-G

Variant names:

• chr3-22432238-A-G
• rs17011371

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 0.0741 in 152,062 control chromosomes in the GnomAD database, including 501 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 0.074 (501 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 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: 0.0742 AC: 11267 AN: 151944 Hom.: 500 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.0743

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0741 AC: 11266 AN: 152062 Hom.: 501 Cov.: 32 AF XY: 0.0743 AC XY: 5523 AN XY: 74334

African (AFR) AF: 0.118 AC: 4894 AN: 41504

American (AMR) AF: 0.0683 AC: 1041 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0669 AC: 232 AN: 3470

East Asian (EAS) AF: 0.0738 AC: 380 AN: 5146

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4826

European-Finnish (FIN) AF: 0.0673 AC: 713 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0536 AC: 3645 AN: 67962

Other (OTH) AF: 0.0756 AC: 159 AN: 2104

Alfa AF: 0.0590 Hom.: 1317

Bravo AF: 0.0786

Asia WGS AF: 0.0630 AC: 219 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	4.5
DANN	Benign	0.57
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs17011371; hg19: chr3-22473729;