chr10-36348093-G-T

Variant names:

• chr10-36348093-G-T
• rs11010633

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 0.267 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.288

Alfa AF: 0.268 Hom.: 3676

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11010633; hg19: chr10-36637021;