18-60384030-G-A

Variant names:

• chr18-60384030-G-A
• rs17066859
• ENST00000650201.1:n.113+54685G>A

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+54685G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,078 control chromosomes in the GnomAD database, including 1,412 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 (1412 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650201.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285681	ENST00000650201.1		n.113+54685G>A		intron	N/A
	ENSG00000285681	ENST00000658928.1		n.156+54685G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16768 AN: 151960 Hom.: 1405 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.0835

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.110 AC: 16795 AN: 152078 Hom.: 1412 Cov.: 32 AF XY: 0.108 AC XY: 8028 AN XY: 74362

African (AFR) AF: 0.229 AC: 9483 AN: 41462

American (AMR) AF: 0.112 AC: 1703 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0908 AC: 315 AN: 3470

East Asian (EAS) AF: 0.0881 AC: 456 AN: 5178

South Asian (SAS) AF: 0.0824 AC: 397 AN: 4820

European-Finnish (FIN) AF: 0.0320 AC: 339 AN: 10602

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

European-Non Finnish (NFE) AF: 0.0561 AC: 3814 AN: 67960

Other (OTH) AF: 0.110 AC: 231 AN: 2108

Alfa AF: 0.0738 Hom.: 757

Bravo AF: 0.127

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.76
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs17066859; hg19: chr18-58051263;