rs10502991

Variant names:

• chr18-54462919-G-A
• rs10502991

Your query was ambiguous. Multiple possible variants found:

• chr18-54462919-G-A
• chr18-54462919-G-T

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 0.166 in 151,818 control chromosomes in the GnomAD database, including 2,349 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 0.17 (2349 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 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: 0.166 AC: 25250 AN: 151700 Hom.: 2348 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0315

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.166 AC: 25259 AN: 151818 Hom.: 2349 Cov.: 31 AF XY: 0.162 AC XY: 12034 AN XY: 74168

African (AFR) AF: 0.242 AC: 10024 AN: 41336

American (AMR) AF: 0.108 AC: 1652 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3466

East Asian (EAS) AF: 0.0313 AC: 162 AN: 5170

South Asian (SAS) AF: 0.121 AC: 580 AN: 4806

European-Finnish (FIN) AF: 0.146 AC: 1543 AN: 10542

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10363 AN: 67926

Other (OTH) AF: 0.146 AC: 308 AN: 2110

Alfa AF: 0.0991 Hom.: 158

Bravo AF: 0.167

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.21
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs10502991; hg19: chr18-51989289;