rs13002041

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;