rs10495857

Variant names:

• chr2-36005590-T-G
• rs10495857

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 0.0331 in 152,294 control chromosomes in the GnomAD database, including 292 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 0.033 (292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• 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 (AMR) allele frequency at 95% confidence interval = 0.146 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: 0.0330 AC: 5022 AN: 152178 Hom.: 282 Cov.: 32

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.0420

Gnomad FIN AF: 0.00961

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00951

Gnomad OTH AF: 0.0310

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

GnomAD4 genome AF: 0.0331 AC: 5045 AN: 152294 Hom.: 292 Cov.: 32 AF XY: 0.0362 AC XY: 2692 AN XY: 74460

African (AFR) AF: 0.0331 AC: 1376 AN: 41578

American (AMR) AF: 0.151 AC: 2304 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3468

East Asian (EAS) AF: 0.0602 AC: 312 AN: 5186

South Asian (SAS) AF: 0.0418 AC: 202 AN: 4828

European-Finnish (FIN) AF: 0.00961 AC: 102 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00951 AC: 647 AN: 68010

Other (OTH) AF: 0.0302 AC: 64 AN: 2116

Alfa AF: 0.0168 Hom.: 153

Bravo AF: 0.0436

Asia WGS AF: 0.0620 AC: 214 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.38
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10495857; hg19: chr2-36232731;