rs734165

Variant names:

• chr10-109938031-C-T
• rs734165

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 0.148 in 152,032 control chromosomes in the GnomAD database, including 2,067 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 0.15 (2067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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: 0.148 AC: 22473 AN: 151914 Hom.: 2068 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.148 AC: 22484 AN: 152032 Hom.: 2067 Cov.: 32 AF XY: 0.153 AC XY: 11333 AN XY: 74310

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.154

Alfa AF: 0.136 Hom.: 278

Bravo AF: 0.141

Asia WGS AF: 0.388 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs734165; hg19: chr10-111697789;