10-44360292-C-T

Variant names:

• chr10-44360292-C-T
• rs11595588

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 0.507 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.281 AC: 11650 AN: 41388

American (AMR) AF: 0.516 AC: 7871 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2142 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2867 AN: 5132

South Asian (SAS) AF: 0.429 AC: 2065 AN: 4808

European-Finnish (FIN) AF: 0.660 AC: 6976 AN: 10562

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41455 AN: 67922

Other (OTH) AF: 0.565 AC: 1193 AN: 2112

Alfa AF: 0.575 Hom.: 60924

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
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11595588; hg19: chr10-44855740;