chr18-38842539-T-C

Variant names:

• chr18-38842539-T-C
• rs10502708

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 0.163 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.167

Alfa AF: 0.176 Hom.: 344

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502708; hg19: chr18-36422503;