rs10496393

Variant names:

• chr2-105446823-G-A
• rs10496393

Your query was ambiguous. Multiple possible variants found:

• chr2-105446823-G-A
• chr2-105446823-G-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 0.0745 in 152,114 control chromosomes in the GnomAD database, including 749 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 0.075 (749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.0745 AC: 11319 AN: 151996 Hom.: 746 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0624

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0745 AC: 11338 AN: 152114 Hom.: 749 Cov.: 32 AF XY: 0.0793 AC XY: 5894 AN XY: 74352

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0624

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.0664

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0323

Gnomad4 OTH AF: 0.0678

Alfa AF: 0.0399 Hom.: 474

Bravo AF: 0.0753

Asia WGS AF: 0.185 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496393; hg19: chr2-106063280;