rs10070190

chr5-26866262-G-Achr5-26866262-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 0.609 in 151,704 control chromosomes in the GnomAD database, including 28,876 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 0.61 (28876 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92272 AN: 151584 Hom.: 28833 Cov.: 30

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.609 AC: 92377 AN: 151704 Hom.: 28876 Cov.: 30 AF XY: 0.614 AC XY: 45475 AN XY: 74118

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.649

Alfa AF: 0.578 Hom.: 5017

Bravo AF: 0.629

Asia WGS AF: 0.812 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.1
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10070190; hg19: chr5-26866371;