10-23375167-G-T

Variant names:

• chr10-23375167-G-T
• rs10734046

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;