rs10496540

Variant names:

• chr2-117448358-C-A
• rs10496540

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 0.12 in 151,938 control chromosomes in the GnomAD database, including 2,223 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 0.12 (2223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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: 0.120 AC: 18162 AN: 151820 Hom.: 2201 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.00926

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0964

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

GnomAD4 genome AF: 0.120 AC: 18225 AN: 151938 Hom.: 2223 Cov.: 32 AF XY: 0.119 AC XY: 8826 AN XY: 74272

African (AFR) AF: 0.311 AC: 12867 AN: 41394

American (AMR) AF: 0.105 AC: 1594 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3468

East Asian (EAS) AF: 0.00909 AC: 47 AN: 5170

South Asian (SAS) AF: 0.124 AC: 595 AN: 4814

European-Finnish (FIN) AF: 0.0413 AC: 436 AN: 10558

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0334 AC: 2273 AN: 67978

Other (OTH) AF: 0.0954 AC: 201 AN: 2108

Alfa AF: 0.0988 Hom.: 207

Bravo AF: 0.131

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.27
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10496540; hg19: chr2-118205934;