18-13190108-C-T

Variant names:

• chr18-13190108-C-T
• rs2027756

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 0.181 in 152,072 control chromosomes in the GnomAD database, including 2,947 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 0.18 (2947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 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: 0.181 AC: 27482 AN: 151954 Hom.: 2942 Cov.: 32

Gnomad AFR AF: 0.0691

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.181 AC: 27493 AN: 152072 Hom.: 2947 Cov.: 32 AF XY: 0.186 AC XY: 13803 AN XY: 74352

African (AFR) AF: 0.0690 AC: 2866 AN: 41516

American (AMR) AF: 0.263 AC: 4017 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1071 AN: 3470

East Asian (EAS) AF: 0.246 AC: 1271 AN: 5174

South Asian (SAS) AF: 0.201 AC: 967 AN: 4820

European-Finnish (FIN) AF: 0.269 AC: 2838 AN: 10550

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13860 AN: 67956

Other (OTH) AF: 0.209 AC: 440 AN: 2104

Alfa AF: 0.197 Hom.: 3547

Bravo AF: 0.175

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2027756; hg19: chr18-13190107;