rs13002041

Variant names:

• chr2-57745699-C-A
• rs13002041

Your query was ambiguous. Multiple possible variants found:

• chr2-57745699-C-A
• chr2-57745699-C-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.595 in 151,818 control chromosomes in the GnomAD database, including 26,973 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 0.59 (26973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 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: 0.595 AC: 90264 AN: 151700 Hom.: 26956 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.595 AC: 90325 AN: 151818 Hom.: 26973 Cov.: 32 AF XY: 0.594 AC XY: 44045 AN XY: 74178

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.601

Alfa AF: 0.580 Hom.: 6832

Bravo AF: 0.586

Asia WGS AF: 0.590 AC: 2051 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	22
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13002041; hg19: chr2-57972834;