rs13009175

chr2-145365368-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;