10-37026293-T-C

Variant names:

• chr10-37026293-T-C
• rs11010995

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 0.0606 in 152,148 control chromosomes in the GnomAD database, including 344 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 0.061 (344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

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 (EAS) allele frequency at 95% confidence interval = 0.0916 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: 0.0607 AC: 9229 AN: 152030 Hom.: 344 Cov.: 32

Gnomad AFR AF: 0.0226

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0986

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0430

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0606 AC: 9226 AN: 152148 Hom.: 344 Cov.: 32 AF XY: 0.0591 AC XY: 4397 AN XY: 74398

Gnomad4 AFR AF: 0.0225

Gnomad4 AMR AF: 0.0745

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0987

Gnomad4 SAS AF: 0.0572

Gnomad4 FIN AF: 0.0430

Gnomad4 NFE AF: 0.0757

Gnomad4 OTH AF: 0.0842

Alfa AF: 0.0782 Hom.: 531

Bravo AF: 0.0640

Asia WGS AF: 0.100 AC: 349 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	2.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11010995; hg19: chr10-37315221;