18-41140781-C-T

Variant names:

• chr18-41140781-C-T
• rs10502750

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 0.271 in 151,044 control chromosomes in the GnomAD database, including 5,972 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 0.27 (5972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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: 0.271 AC: 40962 AN: 150926 Hom.: 5976 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.271 AC: 40975 AN: 151044 Hom.: 5972 Cov.: 32 AF XY: 0.272 AC XY: 20087 AN XY: 73774

African (AFR) AF: 0.171 AC: 7073 AN: 41368

American (AMR) AF: 0.256 AC: 3878 AN: 15122

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 926 AN: 3438

East Asian (EAS) AF: 0.450 AC: 2296 AN: 5102

South Asian (SAS) AF: 0.312 AC: 1499 AN: 4812

European-Finnish (FIN) AF: 0.345 AC: 3635 AN: 10540

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20714 AN: 67358

Other (OTH) AF: 0.289 AC: 607 AN: 2098

Alfa AF: 0.299 Hom.: 11064

Bravo AF: 0.264

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.089
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10502750; hg19: chr18-38720745;