18-60427176-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.563

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1943232; hg19: chr18-58094409;