rs10514090

Variant names:

• chr18-73826896-G-T
• rs10514090

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 0.134 in 152,240 control chromosomes in the GnomAD database, including 1,776 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 0.13 (1776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.179 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: 0.134 AC: 20456 AN: 152122 Hom.: 1777 Cov.: 32

Gnomad AFR AF: 0.0345

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.134 AC: 20465 AN: 152240 Hom.: 1776 Cov.: 32 AF XY: 0.135 AC XY: 10075 AN XY: 74430

African (AFR) AF: 0.0344 AC: 1428 AN: 41570

American (AMR) AF: 0.185 AC: 2829 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3472

East Asian (EAS) AF: 0.133 AC: 691 AN: 5186

South Asian (SAS) AF: 0.117 AC: 565 AN: 4812

European-Finnish (FIN) AF: 0.212 AC: 2247 AN: 10602

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11886 AN: 67992

Other (OTH) AF: 0.136 AC: 286 AN: 2110

Alfa AF: 0.142 Hom.: 1583

Bravo AF: 0.128

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.37
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10514090; hg19: chr18-71494131;