10-121598759-C-T

Variant names:

• chr10-121598759-C-T
• rs1863744

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 0.762 in 152,156 control chromosomes in the GnomAD database, including 45,753 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 0.76 (45753 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 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: 0.762 AC: 115888 AN: 152044 Hom.: 45753 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.762 AC: 115921 AN: 152156 Hom.: 45753 Cov.: 33 AF XY: 0.760 AC XY: 56491 AN XY: 74372

African (AFR) AF: 0.547 AC: 22700 AN: 41484

American (AMR) AF: 0.758 AC: 11588 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3175 AN: 3466

East Asian (EAS) AF: 0.656 AC: 3389 AN: 5164

South Asian (SAS) AF: 0.847 AC: 4089 AN: 4830

European-Finnish (FIN) AF: 0.814 AC: 8629 AN: 10602

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59697 AN: 68006

Other (OTH) AF: 0.790 AC: 1666 AN: 2110

Alfa AF: 0.771 Hom.: 10056

Bravo AF: 0.744

Asia WGS AF: 0.741 AC: 2577 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.55
DANN	Benign	0.96
PhyloP100		-1.6
PromoterAI		-0.061	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1863744; hg19: chr10-123358273;