10-18110590-C-T

Position:

• chr10-18110590-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 0.657 in 151,946 control chromosomes in the GnomAD database, including 33,077 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 0.66 (33077 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99717 AN: 151828 Hom.: 33069 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.657 AC: 99767 AN: 151946 Hom.: 33077 Cov.: 31 AF XY: 0.650 AC XY: 48266 AN XY: 74240

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.672

Alfa AF: 0.676 Hom.: 31832

Bravo AF: 0.665

Asia WGS AF: 0.729 AC: 2536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4748442; hg19: chr10-18399519;