10-117422360-G-T

Variant names:

• chr10-117422360-G-T
• rs181500

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 0.6 in 151,892 control chromosomes in the GnomAD database, including 27,519 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 0.60 (27519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.728 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: 0.600 AC: 91016 AN: 151774 Hom.: 27478 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.600 AC: 91125 AN: 151892 Hom.: 27519 Cov.: 32 AF XY: 0.606 AC XY: 44941 AN XY: 74210

African (AFR) AF: 0.584 AC: 24186 AN: 41420

American (AMR) AF: 0.660 AC: 10076 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2296 AN: 3472

East Asian (EAS) AF: 0.710 AC: 3649 AN: 5136

South Asian (SAS) AF: 0.748 AC: 3602 AN: 4816

European-Finnish (FIN) AF: 0.621 AC: 6541 AN: 10540

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38982 AN: 67934

Other (OTH) AF: 0.607 AC: 1278 AN: 2104

Alfa AF: 0.587 Hom.: 72456

Bravo AF: 0.599

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.64
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs181500; hg19: chr10-119181871;