chr10-117228159-G-T

Position:

• chr10-117228159-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 0.572 in 151,854 control chromosomes in the GnomAD database, including 27,843 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 0.57 (27843 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117228159G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86927 AN: 151736 Hom.: 27841 Cov.: 30

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.572 AC: 86927 AN: 151854 Hom.: 27843 Cov.: 30 AF XY: 0.576 AC XY: 42769 AN XY: 74232

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.601

Alfa AF: 0.679 Hom.: 43799

Bravo AF: 0.543

Asia WGS AF: 0.379 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2532798; hg19: chr10-118987670;