rs10495857

chr2-36005590-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 0.0331 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0331

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.0602

Gnomad4 SAS AF: 0.0418

Gnomad4 FIN AF: 0.00961

Gnomad4 NFE AF: 0.00951

Gnomad4 OTH AF: 0.0302

Alfa AF: 0.0165 Hom.: 65

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495857; hg19: chr2-36232731;