rs17066856

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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.113+53078T>C		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+53078T>C		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0805

Gnomad4 NFE AF: 0.0989

Gnomad4 OTH AF: 0.219

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17066856; hg19: chr18-58049656;