10-117422360-G-T

Position:

• chr10-117422360-G-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 0.6 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.607

Alfa AF: 0.582 Hom.: 24039

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs181500; hg19: chr10-119181871;