rs10502739

Variant names:

• chr18-40640135-C-T
• rs10502739

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 0.121 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• 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

African (AFR) AF: 0.273 AC: 11300 AN: 41354

American (AMR) AF: 0.0693 AC: 1052 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.0993 AC: 344 AN: 3464

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5128

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4820

European-Finnish (FIN) AF: 0.0526 AC: 556 AN: 10568

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0670 AC: 4542 AN: 67792

Other (OTH) AF: 0.0966 AC: 204 AN: 2112

Alfa AF: 0.0820 Hom.: 1361

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10502739; hg19: chr18-38220099;