rs10502708

Variant names:

• chr18-38842539-T-C
• rs10502708

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 0.163 in 152,158 control chromosomes in the GnomAD database, including 2,175 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 0.16 (2175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 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: 0.163 AC: 24742 AN: 152040 Hom.: 2168 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.163 AC: 24777 AN: 152158 Hom.: 2175 Cov.: 32 AF XY: 0.160 AC XY: 11879 AN XY: 74388

African (AFR) AF: 0.122 AC: 5069 AN: 41522

American (AMR) AF: 0.121 AC: 1846 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3466

East Asian (EAS) AF: 0.111 AC: 573 AN: 5164

South Asian (SAS) AF: 0.115 AC: 555 AN: 4812

European-Finnish (FIN) AF: 0.201 AC: 2132 AN: 10596

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13325 AN: 67986

Other (OTH) AF: 0.167 AC: 353 AN: 2112

Alfa AF: 0.175 Hom.: 353

Bravo AF: 0.159

Asia WGS AF: 0.141 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.31
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs10502708; hg19: chr18-36422503;