ENST00000580883.1:n.253+4727A>G

Variant names:

• chr18-27587981-T-C
• rs1420956
• ENST00000580883.1:n.253+4727A>G

Variant summary

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

The ENST00000580883.1(ENSG00000264151):​n.253+4727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,990 control chromosomes in the GnomAD database, including 23,092 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 0.55 (23092 hom., cov: 32)
• Consequence: ENSG00000264151 ENST00000580883.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 7 publications found

Genes affected

ENSG00000264151 (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 (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580883.1. 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
	ENSG00000264151	ENST00000580883.1	TSL:2	n.253+4727A>G		intron	N/A
	ENSG00000264151	ENST00000584546.5	TSL:2	n.216-5966A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82843 AN: 151872 Hom.: 23058 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.546 AC: 82936 AN: 151990 Hom.: 23092 Cov.: 32 AF XY: 0.545 AC XY: 40484 AN XY: 74280

African (AFR) AF: 0.608 AC: 25207 AN: 41464

American (AMR) AF: 0.624 AC: 9536 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3342 AN: 5148

South Asian (SAS) AF: 0.563 AC: 2715 AN: 4822

European-Finnish (FIN) AF: 0.443 AC: 4672 AN: 10540

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.500 AC: 33971 AN: 67958

Other (OTH) AF: 0.543 AC: 1143 AN: 2106

Alfa AF: 0.522 Hom.: 62687

Bravo AF: 0.564

Asia WGS AF: 0.611 AC: 2129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.064
DANN	Benign	0.49
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1420956; hg19: chr18-25167945;