ENST00000580366.1:n.28-13607G>A

Variant names:

• chr18-32899226-G-A
• rs9956150
• ENST00000580366.1:n.28-13607G>A

Variant summary

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

The ENST00000580366.1(ENSG00000263765):​n.28-13607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,214 control chromosomes in the GnomAD database, including 58,715 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 0.85 (58715 hom., cov: 32)
• Consequence: ENSG00000263765 ENST00000580366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 1 publications found

Genes affected

ENSG00000263765 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580366.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000263765	ENST00000580366.1	TSL:3	n.28-13607G>A		intron	N/A
	ENSG00000263765	ENST00000798721.1		n.158+11465G>A		intron	N/A
	ENSG00000263765	ENST00000798722.1		n.424-13668G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129855 AN: 152096 Hom.: 58716 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.853 AC: 129894 AN: 152214 Hom.: 58715 Cov.: 32 AF XY: 0.857 AC XY: 63803 AN XY: 74438

African (AFR) AF: 0.521 AC: 21595 AN: 41474

American (AMR) AF: 0.935 AC: 14301 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.994 AC: 3452 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5153 AN: 5172

South Asian (SAS) AF: 0.992 AC: 4789 AN: 4828

European-Finnish (FIN) AF: 0.970 AC: 10293 AN: 10612

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67236 AN: 68032

Other (OTH) AF: 0.891 AC: 1885 AN: 2116

Alfa AF: 0.894 Hom.: 8185

Bravo AF: 0.835

Asia WGS AF: 0.958 AC: 3328 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.93
DANN	Benign	0.43
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs9956150; hg19: chr18-30479190;