rs17066842

Variant names:

• chr18-60373391-G-A
• rs17066842
• ENST00000650201.1:n.113+44046G>A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000650201.1(ENSG00000285681):​n.113+44046G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0757 in 152,052 control chromosomes in the GnomAD database, including 752 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.076 (752 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 18-60373391-G-A is Benign according to our data. Variant chr18-60373391-G-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 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+44046G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+44046G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0757 AC: 11497 AN: 151940 Hom.: 748 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0369

Gnomad ASJ AF: 0.0240

Gnomad EAS AF: 0.0201

Gnomad SAS AF: 0.0349

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0757 AC: 11512 AN: 152052 Hom.: 752 Cov.: 32 AF XY: 0.0743 AC XY: 5527 AN XY: 74342

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.0368

Gnomad4 ASJ AF: 0.0240

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.0339

Gnomad4 FIN AF: 0.0245

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0780 Hom.: 123

Bravo AF: 0.0817

Asia WGS AF: 0.0270 AC: 93 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17066842; hg19: chr18-58040624;