18-28335176-A-G

Variant names:

• chr18-28335176-A-G
• rs1464612

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 0.108 in 152,176 control chromosomes in the GnomAD database, including 1,443 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 0.11 (1443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 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: 0.108 AC: 16397 AN: 152058 Hom.: 1430 Cov.: 32

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.108 AC: 16417 AN: 152176 Hom.: 1443 Cov.: 32 AF XY: 0.113 AC XY: 8411 AN XY: 74386

African (AFR) AF: 0.0489 AC: 2031 AN: 41550

American (AMR) AF: 0.253 AC: 3867 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1895 AN: 5142

South Asian (SAS) AF: 0.125 AC: 603 AN: 4826

European-Finnish (FIN) AF: 0.134 AC: 1421 AN: 10590

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0870 AC: 5917 AN: 68010

Other (OTH) AF: 0.107 AC: 225 AN: 2112

Alfa AF: 0.0979 Hom.: 2305

Bravo AF: 0.120

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs1464612; hg19: chr18-25915140;