10-36880367-G-T

Variant names:

• chr10-36880367-G-T
• rs1192691

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.879 AC: 36462 AN: 41496

American (AMR) AF: 0.882 AC: 13477 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3215 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2165 AN: 5150

South Asian (SAS) AF: 0.744 AC: 3578 AN: 4812

European-Finnish (FIN) AF: 0.914 AC: 9658 AN: 10562

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64265 AN: 68020

Other (OTH) AF: 0.884 AC: 1868 AN: 2114

Alfa AF: 0.924 Hom.: 157552

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1192691; hg19: chr10-37169295;