18-27490391-G-T

Variant names:

• chr18-27490391-G-T
• rs4800279
• ENST00000584546.5:n.447+11288C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000584546.5(ENSG00000264151):​n.447+11288C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 151,922 control chromosomes in the GnomAD database, including 828 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 0.087 (828 hom., cov: 32)
• Consequence: ENSG00000264151 ENST00000584546.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

Genes affected

ENSG00000264151 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264151	ENST00000584546.5	n.447+11288C>A		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13226 AN: 151806 Hom.: 828 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.0872 AC: 13251 AN: 151922 Hom.: 828 Cov.: 32 AF XY: 0.0852 AC XY: 6327 AN XY: 74254

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.0882

Gnomad4 ASJ AF: 0.0842

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0370

Gnomad4 FIN AF: 0.0544

Gnomad4 NFE AF: 0.0526

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.0557 Hom.: 290

Bravo AF: 0.0963

Asia WGS AF: 0.0310 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4800279; hg19: chr18-25070355;