rs10502739

Variant names:

• chr18-40640135-C-T
• rs10502739

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 0.121 in 151,632 control chromosomes in the GnomAD database, including 1,772 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 0.12 (1772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.120 AC: 18232 AN: 151514 Hom.: 1765 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.0993

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.121 AC: 18277 AN: 151632 Hom.: 1772 Cov.: 32 AF XY: 0.118 AC XY: 8707 AN XY: 74100

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0693

Gnomad4 ASJ AF: 0.0993

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.0966

Alfa AF: 0.0761 Hom.: 820

Bravo AF: 0.128

Asia WGS AF: 0.0320 AC: 112 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502739; hg19: chr18-38220099;