rs2059915

Variant names:

• chr2-41633814-T-G
• rs2059915

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 0.669 in 151,978 control chromosomes in the GnomAD database, including 34,375 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 0.67 (34375 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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: 0.669 AC: 101657 AN: 151862 Hom.: 34373 Cov.: 31

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.669 AC: 101697 AN: 151978 Hom.: 34375 Cov.: 31 AF XY: 0.670 AC XY: 49797 AN XY: 74286

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.650

Alfa AF: 0.642 Hom.: 9661

Bravo AF: 0.664

Asia WGS AF: 0.643 AC: 2234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2059915; hg19: chr2-41860954;