10-123121986-T-C

Variant names:

• chr10-123121986-T-C
• rs10794595

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 0.63 in 152,116 control chromosomes in the GnomAD database, including 30,789 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 0.63 (30789 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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: 0.631 AC: 95856 AN: 151996 Hom.: 30769 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.630 AC: 95907 AN: 152116 Hom.: 30789 Cov.: 33 AF XY: 0.637 AC XY: 47386 AN XY: 74366

African (AFR) AF: 0.514 AC: 21334 AN: 41490

American (AMR) AF: 0.697 AC: 10652 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2664 AN: 3470

East Asian (EAS) AF: 0.859 AC: 4439 AN: 5170

South Asian (SAS) AF: 0.811 AC: 3912 AN: 4822

European-Finnish (FIN) AF: 0.620 AC: 6558 AN: 10580

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44124 AN: 67984

Other (OTH) AF: 0.654 AC: 1381 AN: 2112

Alfa AF: 0.649 Hom.: 95892

Bravo AF: 0.632

Asia WGS AF: 0.813 AC: 2825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.42
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10794595; hg19: chr10-124881502;