10-18110590-C-T

Variant names:

• chr10-18110590-C-T
• rs4748442

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 0.657 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.612 AC: 25332 AN: 41412

American (AMR) AF: 0.641 AC: 9790 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2466 AN: 3470

East Asian (EAS) AF: 0.829 AC: 4281 AN: 5162

South Asian (SAS) AF: 0.690 AC: 3319 AN: 4808

European-Finnish (FIN) AF: 0.525 AC: 5529 AN: 10524

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46800 AN: 67972

Other (OTH) AF: 0.672 AC: 1420 AN: 2114

Alfa AF: 0.673 Hom.: 41913

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4748442; hg19: chr10-18399519;