rs10514193

Variant names:

• chr18-75896786-C-G
• rs10514193

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 0.136 in 152,204 control chromosomes in the GnomAD database, including 2,477 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 0.14 (2477 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 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: 0.136 AC: 20610 AN: 152086 Hom.: 2460 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0445

Gnomad SAS AF: 0.0614

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0609

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.136 AC: 20666 AN: 152204 Hom.: 2477 Cov.: 32 AF XY: 0.135 AC XY: 10014 AN XY: 74430

African (AFR) AF: 0.321 AC: 13320 AN: 41492

American (AMR) AF: 0.0592 AC: 906 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.0446 AC: 231 AN: 5182

South Asian (SAS) AF: 0.0615 AC: 297 AN: 4830

European-Finnish (FIN) AF: 0.108 AC: 1141 AN: 10600

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0609 AC: 4143 AN: 68020

Other (OTH) AF: 0.111 AC: 234 AN: 2110

Alfa AF: 0.108 Hom.: 188

Bravo AF: 0.143

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10514193; hg19: chr18-73608741;