chr13-22031441-A-G

Variant names:

• chr13-22031441-A-G
• rs3117915

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 0.353 in 151,958 control chromosomes in the GnomAD database, including 11,488 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 0.35 (11488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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: 0.353 AC: 53636 AN: 151840 Hom.: 11470 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.353 AC: 53713 AN: 151958 Hom.: 11488 Cov.: 32 AF XY: 0.353 AC XY: 26199 AN XY: 74276

African (AFR) AF: 0.565 AC: 23357 AN: 41370

American (AMR) AF: 0.343 AC: 5239 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3845 AN: 5160

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4818

European-Finnish (FIN) AF: 0.248 AC: 2624 AN: 10580

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15466 AN: 67980

Other (OTH) AF: 0.339 AC: 715 AN: 2108

Alfa AF: 0.275 Hom.: 29716

Bravo AF: 0.372

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.28
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs3117915; hg19: chr13-22605580;