rs10502812

Variant names:

• chr18-43480953-G-A
• rs10502812

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 0.173 in 152,036 control chromosomes in the GnomAD database, including 2,551 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 (2551 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 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: 0.173 AC: 26337 AN: 151918 Hom.: 2546 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.173 AC: 26362 AN: 152036 Hom.: 2551 Cov.: 32 AF XY: 0.178 AC XY: 13223 AN XY: 74292

African (AFR) AF: 0.118 AC: 4886 AN: 41494

American (AMR) AF: 0.256 AC: 3916 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3466

East Asian (EAS) AF: 0.320 AC: 1649 AN: 5146

South Asian (SAS) AF: 0.154 AC: 740 AN: 4816

European-Finnish (FIN) AF: 0.231 AC: 2435 AN: 10544

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11507 AN: 67984

Other (OTH) AF: 0.186 AC: 393 AN: 2110

Alfa AF: 0.165 Hom.: 274

Bravo AF: 0.171

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10502812; hg19: chr18-41060918;