rs17066859

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr18-60384030-G-A
• chr18-60384030-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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+54685G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+54685G>A		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0908

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.0824

Gnomad4 FIN AF: 0.0320

Gnomad4 NFE AF: 0.0561

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0722 Hom.: 608

Bravo AF: 0.127

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17066859; hg19: chr18-58051263;