rs10495742

Variant names:

• chr2-23327373-T-C
• rs10495742

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.188 in 152,144 control chromosomes in the GnomAD database, including 3,049 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 0.19 (3049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 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: 0.188 AC: 28611 AN: 152028 Hom.: 3043 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.188 AC: 28620 AN: 152144 Hom.: 3049 Cov.: 32 AF XY: 0.188 AC XY: 13973 AN XY: 74382

African (AFR) AF: 0.104 AC: 4319 AN: 41522

American (AMR) AF: 0.145 AC: 2215 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 661 AN: 3472

East Asian (EAS) AF: 0.172 AC: 889 AN: 5170

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4822

European-Finnish (FIN) AF: 0.250 AC: 2639 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16264 AN: 67978

Other (OTH) AF: 0.203 AC: 427 AN: 2106

Alfa AF: 0.220 Hom.: 16071

Bravo AF: 0.175

Asia WGS AF: 0.208 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10495742; hg19: chr2-23550244;