rs12251841

Positions:

• chr10-94934381-C-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 0.192 in 150,044 control chromosomes in the GnomAD database, including 2,953 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 (2953 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.192 AC: 28766 AN: 149928 Hom.: 2952 Cov.: 28

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00920

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.192 AC: 28764 AN: 150044 Hom.: 2953 Cov.: 28 AF XY: 0.189 AC XY: 13818 AN XY: 73184

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.00922

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.189

Alfa AF: 0.216 Hom.: 444

Bravo AF: 0.187

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.43
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12251841; hg19: chr10-96694138; COSMIC: COSV53249068;