rs13009175

Variant names:

• chr2-145365368-C-T
• rs13009175

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 0.546 in 151,306 control chromosomes in the GnomAD database, including 22,794 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 0.55 (22794 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.611 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: 0.546 AC: 82605 AN: 151198 Hom.: 22783 Cov.: 30

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.546 AC: 82648 AN: 151306 Hom.: 22794 Cov.: 30 AF XY: 0.542 AC XY: 40069 AN XY: 73880

African (AFR) AF: 0.565 AC: 23329 AN: 41306

American (AMR) AF: 0.622 AC: 9441 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2049 AN: 3464

East Asian (EAS) AF: 0.548 AC: 2821 AN: 5150

South Asian (SAS) AF: 0.560 AC: 2699 AN: 4818

European-Finnish (FIN) AF: 0.426 AC: 4438 AN: 10412

Middle Eastern (MID) AF: 0.601 AC: 173 AN: 288

European-Non Finnish (NFE) AF: 0.532 AC: 36022 AN: 67680

Other (OTH) AF: 0.541 AC: 1131 AN: 2092

Alfa AF: 0.561 Hom.: 4096

Bravo AF: 0.560

Asia WGS AF: 0.552 AC: 1912 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.28
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs13009175; hg19: chr2-146122936;