18-13191185-C-T

Variant names:

• chr18-13191185-C-T
• rs12969041

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 0.437 in 152,050 control chromosomes in the GnomAD database, including 14,698 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 0.44 (14698 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.442 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: 0.438 AC: 66470 AN: 151930 Hom.: 14691 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.437 AC: 66497 AN: 152050 Hom.: 14698 Cov.: 32 AF XY: 0.437 AC XY: 32448 AN XY: 74314

African (AFR) AF: 0.447 AC: 18546 AN: 41466

American (AMR) AF: 0.447 AC: 6834 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1264 AN: 5172

South Asian (SAS) AF: 0.331 AC: 1598 AN: 4822

European-Finnish (FIN) AF: 0.486 AC: 5129 AN: 10548

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29943 AN: 67980

Other (OTH) AF: 0.448 AC: 947 AN: 2112

Alfa AF: 0.438 Hom.: 62202

Bravo AF: 0.435

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.079
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12969041; hg19: chr18-13191184;