rs10514193

chr18-75896786-C-G

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 0.136 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.0446

Gnomad4 SAS AF: 0.0615

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0609

Gnomad4 OTH AF: 0.111

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514193; hg19: chr18-73608741;