10-36582968-T-G

Variant names:

• chr10-36582968-T-G
• rs2151173

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 0.854 in 152,028 control chromosomes in the GnomAD database, including 55,704 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 0.85 (55704 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 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: 0.854 AC: 129790 AN: 151910 Hom.: 55672 Cov.: 30

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.854 AC: 129871 AN: 152028 Hom.: 55704 Cov.: 30 AF XY: 0.856 AC XY: 63609 AN XY: 74324

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.834

Alfa AF: 0.883 Hom.: 31827

Bravo AF: 0.838

Asia WGS AF: 0.809 AC: 2812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2151173; hg19: chr10-36871896;