18-60373245-G-A

Variant names:

• chr18-60373245-G-A
• rs8087522
• ENST00000650201.1:n.113+43900G>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+43900G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,896 control chromosomes in the GnomAD database, including 12,477 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 0.38 (12477 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 20 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 = 0.592 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285681	ENST00000650201.1		n.113+43900G>A		intron	N/A
	ENSG00000285681	ENST00000658928.1		n.156+43900G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57467 AN: 151776 Hom.: 12442 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.379 AC: 57541 AN: 151896 Hom.: 12477 Cov.: 32 AF XY: 0.370 AC XY: 27464 AN XY: 74216

African (AFR) AF: 0.598 AC: 24767 AN: 41390

American (AMR) AF: 0.314 AC: 4798 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3472

East Asian (EAS) AF: 0.132 AC: 682 AN: 5178

South Asian (SAS) AF: 0.281 AC: 1356 AN: 4828

European-Finnish (FIN) AF: 0.264 AC: 2780 AN: 10530

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21073 AN: 67920

Other (OTH) AF: 0.345 AC: 727 AN: 2106

Alfa AF: 0.348 Hom.: 16598

Bravo AF: 0.397

Asia WGS AF: 0.235 AC: 816 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.36
DANN	Benign	0.46
PhyloP100		-0.66
PromoterAI		0.0020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8087522; hg19: chr18-58040478;