rs10496393

chr2-105446823-G-Achr2-105446823-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;