rs10496605

chr2-123042772-G-Achr2-123042772-G-T

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 0.109 in 151,604 control chromosomes in the GnomAD database, including 2,032 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 0.11 (2032 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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: 0.109 AC: 16528 AN: 151484 Hom.: 2033 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0660

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.109 AC: 16551 AN: 151604 Hom.: 2032 Cov.: 32 AF XY: 0.108 AC XY: 8035 AN XY: 74080

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.0598

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0819

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0202

Gnomad4 OTH AF: 0.0905

Alfa AF: 0.0271 Hom.: 61

Bravo AF: 0.122

Asia WGS AF: 0.135 AC: 464 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.1
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496605; hg19: chr2-123800348;