10-36348093-G-T

Variant names:

• chr10-36348093-G-T
• rs11010633

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 0.267 in 151,852 control chromosomes in the GnomAD database, including 5,577 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 0.27 (5577 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 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: 0.267 AC: 40565 AN: 151734 Hom.: 5577 Cov.: 31

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.267 AC: 40582 AN: 151852 Hom.: 5577 Cov.: 31 AF XY: 0.266 AC XY: 19715 AN XY: 74194

African (AFR) AF: 0.259 AC: 10730 AN: 41372

American (AMR) AF: 0.197 AC: 3015 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3470

East Asian (EAS) AF: 0.163 AC: 840 AN: 5152

South Asian (SAS) AF: 0.315 AC: 1520 AN: 4820

European-Finnish (FIN) AF: 0.291 AC: 3068 AN: 10532

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19172 AN: 67924

Other (OTH) AF: 0.288 AC: 607 AN: 2108

Alfa AF: 0.268 Hom.: 5386

Bravo AF: 0.257

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.51
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs11010633; hg19: chr10-36637021;