chr10-94934381-C-T

Variant names:

• chr10-94934381-C-T
• rs12251841

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 0.192 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.197 AC: 8039 AN: 40848

American (AMR) AF: 0.130 AC: 1948 AN: 15024

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3462

East Asian (EAS) AF: 0.00922 AC: 47 AN: 5098

South Asian (SAS) AF: 0.164 AC: 782 AN: 4768

European-Finnish (FIN) AF: 0.181 AC: 1818 AN: 10050

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.218 AC: 14698 AN: 67540

Other (OTH) AF: 0.189 AC: 390 AN: 2068

Alfa AF: 0.216 Hom.: 463

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

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