rs10496611

Positions:

• chr2-123373968-G-A
• chr2-123373968-G-C
• chr2-123373968-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 0.297 in 151,866 control chromosomes in the GnomAD database, including 7,193 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 0.30 (7193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

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 (EAS) allele frequency at 95% confidence interval = 0.404 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: 0.298 AC: 45153 AN: 151748 Hom.: 7190 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.297 AC: 45155 AN: 151866 Hom.: 7193 Cov.: 32 AF XY: 0.302 AC XY: 22414 AN XY: 74208

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.294

Alfa AF: 0.300 Hom.: 3972

Bravo AF: 0.278

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496611; hg19: chr2-124131544;