10-18110590-C-T

Variant names:

• chr10-18110590-C-T
• rs4748442

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;