18-14583729-T-C

Variant names:

• chr18-14583729-T-C
• rs1846090
• ENST00000794858.1:n.277+8357A>G

Variant summary

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

The ENST00000794858.1(ENSG00000303474):​n.277+8357A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,896 control chromosomes in the GnomAD database, including 7,212 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 0.30 (7212 hom., cov: 31)
• Consequence: ENSG00000303474 ENST00000794858.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 2 publications found

Genes affected

ENSG00000303474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794858.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303474	ENST00000794858.1		n.277+8357A>G		intron	N/A
	ENSG00000303474	ENST00000794859.1		n.278-6545A>G		intron	N/A
	ENSG00000303474	ENST00000794860.1		n.626+18412A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45056 AN: 151778 Hom.: 7206 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.297 AC: 45081 AN: 151896 Hom.: 7212 Cov.: 31 AF XY: 0.293 AC XY: 21726 AN XY: 74234

African (AFR) AF: 0.206 AC: 8537 AN: 41430

American (AMR) AF: 0.261 AC: 3984 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3470

East Asian (EAS) AF: 0.172 AC: 887 AN: 5156

South Asian (SAS) AF: 0.289 AC: 1391 AN: 4820

European-Finnish (FIN) AF: 0.330 AC: 3479 AN: 10530

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24550 AN: 67932

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.341 Hom.: 4735

Bravo AF: 0.285

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.68
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs1846090; hg19: chr18-14583728;