rs2059915

Positions:

• chr2-41633814-T-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;