18-32543605-G-A

Variant names:

• chr18-32543605-G-A
• rs1648663
• ENST00000646805.1:n.360-17030G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646805.1(ENSG00000285095):​n.360-17030G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,114 control chromosomes in the GnomAD database, including 44,826 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 0.76 (44826 hom., cov: 33)
• Consequence: ENSG00000285095 ENST00000646805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 2 publications found

Genes affected

ENSG00000285095 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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
ENSG00000285095	ENST00000646805.1	n.360-17030G>A		intron_variant	Intron 2 of 6
ENSG00000285095	ENST00000654761.1	n.184+25638G>A		intron_variant	Intron 2 of 2
ENSG00000285095	ENST00000716676.1	n.275+25638G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115380 AN: 151996 Hom.: 44809 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.759 AC: 115435 AN: 152114 Hom.: 44826 Cov.: 33 AF XY: 0.762 AC XY: 56632 AN XY: 74354

African (AFR) AF: 0.567 AC: 23485 AN: 41438

American (AMR) AF: 0.854 AC: 13056 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2808 AN: 3472

East Asian (EAS) AF: 0.895 AC: 4625 AN: 5170

South Asian (SAS) AF: 0.804 AC: 3878 AN: 4822

European-Finnish (FIN) AF: 0.837 AC: 8859 AN: 10580

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56076 AN: 68018

Other (OTH) AF: 0.777 AC: 1641 AN: 2112

Alfa AF: 0.797 Hom.: 106188

Bravo AF: 0.754

Asia WGS AF: 0.853 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.55
DANN	Benign	0.55
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1648663; hg19: chr18-30123568;