10-36880367-G-T

Variant names:

• chr10-36880367-G-T
• rs1192691

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 0.893 in 152,110 control chromosomes in the GnomAD database, including 61,454 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 0.89 (61454 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 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: 0.893 AC: 135735 AN: 151992 Hom.: 61391 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.893 AC: 135856 AN: 152110 Hom.: 61454 Cov.: 31 AF XY: 0.885 AC XY: 65805 AN XY: 74342

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.884

Alfa AF: 0.927 Hom.: 58266

Bravo AF: 0.890

Asia WGS AF: 0.640 AC: 2228 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	0.072
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1192691; hg19: chr10-37169295;