chr18-60373391-G-A

Variant names:

• chr18-60373391-G-A
• rs17066842
• ENST00000650201.1:n.113+44046G>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+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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.076 (752 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943
• Publications: 16 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=-0.89).
• 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

African (AFR) AF: 0.182 AC: 7563 AN: 41456

American (AMR) AF: 0.0368 AC: 563 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0240 AC: 83 AN: 3464

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5172

South Asian (SAS) AF: 0.0339 AC: 163 AN: 4810

European-Finnish (FIN) AF: 0.0245 AC: 259 AN: 10560

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0379 AC: 2575 AN: 67986

Other (OTH) AF: 0.0662 AC: 140 AN: 2114

Alfa AF: 0.0566 Hom.: 567

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
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs17066842; hg19: chr18-58040624;