18-895115-C-T

Variant names:

• chr18-895115-C-T
• rs4798684
• ENST00000582554.2:n.179-420G>A

Variant summary

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

The ENST00000582554.2(ENSG00000265179):​n.179-420G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,066 control chromosomes in the GnomAD database, including 31,153 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 0.62 (31153 hom., cov: 34)
• Consequence: ENSG00000265179 ENST00000582554.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 4 publications found

Genes affected

ENSG00000265179 (HGNC:):

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 = 0.763 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
ENSG00000265179	ENST00000582554.2	n.179-420G>A		intron_variant	Intron 1 of 1	5
ENSG00000265179	ENST00000717225.1	n.262-420G>A		intron_variant	Intron 1 of 1
ENSG00000265179	ENST00000717226.1	n.341-420G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94049 AN: 151948 Hom.: 31150 Cov.: 34

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.619 AC: 94080 AN: 152066 Hom.: 31153 Cov.: 34 AF XY: 0.622 AC XY: 46214 AN XY: 74338

African (AFR) AF: 0.364 AC: 15096 AN: 41470

American (AMR) AF: 0.719 AC: 10995 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2475 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4066 AN: 5190

South Asian (SAS) AF: 0.772 AC: 3728 AN: 4830

European-Finnish (FIN) AF: 0.660 AC: 6958 AN: 10542

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.714 AC: 48533 AN: 67966

Other (OTH) AF: 0.651 AC: 1374 AN: 2110

Alfa AF: 0.649 Hom.: 4350

Bravo AF: 0.610

Asia WGS AF: 0.732 AC: 2529 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4798684; hg19: chr18-895116;