rs13009175

Variant names:

• chr2-145365368-C-T
• rs13009175

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.541

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13009175; hg19: chr2-146122936;