ENST00000589662.1:n.364+482C>A

Variant names:

• chr18-55787138-C-A
• rs4996482
• ENST00000589662.1:n.364+482C>A

Variant summary

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

The ENST00000589662.1(ENSG00000267284):​n.364+482C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,086 control chromosomes in the GnomAD database, including 5,827 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 0.26 (5827 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000589662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 5 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589662.1. 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
	ENSG00000267284	ENST00000589662.1	TSL:5	n.364+482C>A		intron	N/A
	ENSG00000267284	ENST00000654829.1		n.303+482C>A		intron	N/A
	ENSG00000267284	ENST00000729561.1		n.547+482C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39953 AN: 151968 Hom.: 5821 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.263 AC: 39998 AN: 152086 Hom.: 5827 Cov.: 32 AF XY: 0.263 AC XY: 19518 AN XY: 74330

African (AFR) AF: 0.142 AC: 5904 AN: 41498

American (AMR) AF: 0.384 AC: 5857 AN: 15266

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

East Asian (EAS) AF: 0.178 AC: 919 AN: 5168

South Asian (SAS) AF: 0.175 AC: 844 AN: 4818

European-Finnish (FIN) AF: 0.274 AC: 2900 AN: 10566

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21744 AN: 67980

Other (OTH) AF: 0.267 AC: 565 AN: 2114

Alfa AF: 0.304 Hom.: 20133

Bravo AF: 0.267

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.6
DANN	Benign	0.83
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4996482; hg19: chr18-53454369;