chr18-60427176-A-G

Variant names:

• chr18-60427176-A-G
• rs1943232
• ENST00000650201.1:n.114-52395A>G

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.114-52395A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,704 control chromosomes in the GnomAD database, including 25,667 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 0.58 (25667 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943
• Publications: 2 publications found

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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
ENSG00000285681	ENST00000650201.1	n.114-52395A>G		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.157-52395A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87871 AN: 151586 Hom.: 25663 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.579 AC: 87911 AN: 151704 Hom.: 25667 Cov.: 32 AF XY: 0.581 AC XY: 43043 AN XY: 74116

African (AFR) AF: 0.571 AC: 23664 AN: 41416

American (AMR) AF: 0.578 AC: 8806 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1785 AN: 3464

East Asian (EAS) AF: 0.759 AC: 3913 AN: 5156

South Asian (SAS) AF: 0.485 AC: 2338 AN: 4816

European-Finnish (FIN) AF: 0.595 AC: 6258 AN: 10510

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39386 AN: 67800

Other (OTH) AF: 0.563 AC: 1186 AN: 2106

Alfa AF: 0.581 Hom.: 3282

Bravo AF: 0.576

Asia WGS AF: 0.613 AC: 2131 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.63
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs1943232; hg19: chr18-58094409;