18-40854820-C-T

Variant names:

• chr18-40854820-C-T
• rs1982037

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 0.116 in 152,096 control chromosomes in the GnomAD database, including 1,269 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 (1269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 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: 0.116 AC: 17660 AN: 151978 Hom.: 1269 Cov.: 32

Gnomad AFR AF: 0.0410

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.116 AC: 17654 AN: 152096 Hom.: 1269 Cov.: 32 AF XY: 0.117 AC XY: 8673 AN XY: 74346

African (AFR) AF: 0.0408 AC: 1691 AN: 41478

American (AMR) AF: 0.129 AC: 1964 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 668 AN: 3472

East Asian (EAS) AF: 0.0673 AC: 348 AN: 5174

South Asian (SAS) AF: 0.150 AC: 722 AN: 4812

European-Finnish (FIN) AF: 0.138 AC: 1458 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10371 AN: 67996

Other (OTH) AF: 0.136 AC: 288 AN: 2110

Alfa AF: 0.127 Hom.: 1432

Bravo AF: 0.111

Asia WGS AF: 0.0910 AC: 314 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.66
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1982037; hg19: chr18-38434784;