18-28206916-C-T

Variant names:

• chr18-28206916-C-T
• rs11659841

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 0.812 in 152,140 control chromosomes in the GnomAD database, including 50,273 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 0.81 (50273 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.85 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: 0.812 AC: 123374 AN: 152022 Hom.: 50228 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.812 AC: 123482 AN: 152140 Hom.: 50273 Cov.: 32 AF XY: 0.808 AC XY: 60089 AN XY: 74360

African (AFR) AF: 0.757 AC: 31432 AN: 41500

American (AMR) AF: 0.839 AC: 12817 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2864 AN: 3472

East Asian (EAS) AF: 0.724 AC: 3740 AN: 5164

South Asian (SAS) AF: 0.767 AC: 3699 AN: 4820

European-Finnish (FIN) AF: 0.756 AC: 7995 AN: 10578

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58177 AN: 68006

Other (OTH) AF: 0.842 AC: 1781 AN: 2114

Alfa AF: 0.849 Hom.: 56713

Bravo AF: 0.818

Asia WGS AF: 0.746 AC: 2593 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	1.1
DANN	Benign	0.59
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs11659841; hg19: chr18-25786880;