rs10932058

Positions:

• chr2-204332163-A-C

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 0.465 in 152,022 control chromosomes in the GnomAD database, including 16,612 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 0.46 (16612 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 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: 0.465 AC: 70577 AN: 151904 Hom.: 16598 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.465 AC: 70640 AN: 152022 Hom.: 16612 Cov.: 32 AF XY: 0.459 AC XY: 34154 AN XY: 74338

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.489

Alfa AF: 0.490 Hom.: 10891

Bravo AF: 0.466

Asia WGS AF: 0.364 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10932058; hg19: chr2-205196886;