10-44360292-C-T

Position:

• chr10-44360292-C-T

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 0.507 in 151,854 control chromosomes in the GnomAD database, including 21,108 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 0.51 (21108 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76988 AN: 151736 Hom.: 21101 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.507 AC: 77003 AN: 151854 Hom.: 21108 Cov.: 31 AF XY: 0.510 AC XY: 37815 AN XY: 74206

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.565

Alfa AF: 0.584 Hom.: 46399

Bravo AF: 0.490

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11595588; hg19: chr10-44855740;