rs17066856

Variant names:

• chr18-60382423-T-C
• rs17066856
• ENST00000650201.1:n.113+53078T>C

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+53078T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 134,694 control chromosomes in the GnomAD database, including 5,898 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 0.23 (5898 hom., cov: 31)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 18 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285681	ENST00000650201.1		n.113+53078T>C		intron	N/A
	ENSG00000285681	ENST00000658928.1		n.156+53078T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 31569 AN: 134574 Hom.: 5865 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.235 AC: 31646 AN: 134694 Hom.: 5898 Cov.: 31 AF XY: 0.234 AC XY: 15104 AN XY: 64612

African (AFR) AF: 0.530 AC: 20723 AN: 39122

American (AMR) AF: 0.195 AC: 2359 AN: 12068

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 324 AN: 3160

East Asian (EAS) AF: 0.105 AC: 461 AN: 4392

South Asian (SAS) AF: 0.153 AC: 558 AN: 3638

European-Finnish (FIN) AF: 0.0805 AC: 632 AN: 7848

Middle Eastern (MID) AF: 0.103 AC: 28 AN: 272

European-Non Finnish (NFE) AF: 0.0989 AC: 6093 AN: 61630

Other (OTH) AF: 0.219 AC: 380 AN: 1738

Alfa AF: 0.139 Hom.: 565

Bravo AF: 0.234

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.50
PhyloP100		0.014

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17066856;

hg19: chr18-58049656;