chr10-23375167-G-T

Position:

• chr10-23375167-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 0.657 in 152,030 control chromosomes in the GnomAD database, including 35,175 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 0.66 (35175 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23375167G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99746 AN: 151912 Hom.: 35102 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.657 AC: 99883 AN: 152030 Hom.: 35175 Cov.: 31 AF XY: 0.659 AC XY: 48965 AN XY: 74298

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.635

Alfa AF: 0.543 Hom.: 29679

Bravo AF: 0.685

Asia WGS AF: 0.723 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10734046; hg19: chr10-23664096;