rs10932058

Variant names:

• chr2-204332163-A-C
• rs10932058

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.439 AC: 18213 AN: 41454

American (AMR) AF: 0.461 AC: 7046 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2001 AN: 3464

East Asian (EAS) AF: 0.350 AC: 1808 AN: 5164

South Asian (SAS) AF: 0.365 AC: 1761 AN: 4826

European-Finnish (FIN) AF: 0.405 AC: 4272 AN: 10558

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34096 AN: 67960

Other (OTH) AF: 0.489 AC: 1032 AN: 2110

Alfa AF: 0.491 Hom.: 11857

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10932058; hg19: chr2-205196886;