18-59938389-A-G

Variant names:

• chr18-59938389-A-G
• rs7407281
• ENST00000789570.1:n.315+385A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789570.1(ENSG00000302789):​n.315+385A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 149,696 control chromosomes in the GnomAD database, including 43,431 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 0.76 (43431 hom., cov: 25)
• Consequence: ENSG00000302789 ENST00000789570.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 6 publications found

Genes affected

ENSG00000302789 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789570.1. 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
	ENSG00000302789	ENST00000789570.1		n.315+385A>G		intron	N/A
	ENSG00000302789	ENST00000789571.1		n.198-3841A>G		intron	N/A
	ENSG00000302789	ENST00000789572.1		n.199-7371A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.760 AC: 113646 AN: 149582 Hom.: 43400 Cov.: 25

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.760 AC: 113727 AN: 149696 Hom.: 43431 Cov.: 25 AF XY: 0.760 AC XY: 55340 AN XY: 72800

African (AFR) AF: 0.676 AC: 27412 AN: 40548

American (AMR) AF: 0.746 AC: 11194 AN: 15006

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2926 AN: 3468

East Asian (EAS) AF: 0.656 AC: 3312 AN: 5050

South Asian (SAS) AF: 0.792 AC: 3777 AN: 4766

European-Finnish (FIN) AF: 0.834 AC: 8215 AN: 9850

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54354 AN: 67722

Other (OTH) AF: 0.780 AC: 1626 AN: 2084

Alfa AF: 0.801 Hom.: 53624

Bravo AF: 0.749

Asia WGS AF: 0.741 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.91
DANN	Benign	0.85
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7407281; hg19: chr18-57605621;