18-55084786-G-A

Variant names:

• chr18-55084786-G-A
• rs12966547
• ENST00000774238.1:n.317-33102G>A

Variant summary

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

The ENST00000774238.1(ENSG00000300819):​n.317-33102G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,012 control chromosomes in the GnomAD database, including 11,905 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 0.39 (11905 hom., cov: 32)
• Consequence: ENSG00000300819 ENST00000774238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.900
• Publications: 53 publications found

Genes affected

ENSG00000300819 (HGNC:):

LINC03035 (HGNC:56211): (long intergenic non-protein coding RNA 3035)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774238.1. 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
	ENSG00000300819	ENST00000774238.1		n.317-33102G>A		intron	N/A
	ENSG00000300838	ENST00000774358.1		n.449+2112C>T		intron	N/A
	ENSG00000300838	ENST00000774359.1		n.138-5506C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59815 AN: 151894 Hom.: 11896 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.394 AC: 59854 AN: 152012 Hom.: 11905 Cov.: 32 AF XY: 0.394 AC XY: 29263 AN XY: 74276

African (AFR) AF: 0.345 AC: 14304 AN: 41452

American (AMR) AF: 0.407 AC: 6215 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3470

East Asian (EAS) AF: 0.609 AC: 3139 AN: 5154

South Asian (SAS) AF: 0.288 AC: 1385 AN: 4816

European-Finnish (FIN) AF: 0.438 AC: 4616 AN: 10550

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27478 AN: 67976

Other (OTH) AF: 0.380 AC: 802 AN: 2110

Alfa AF: 0.407 Hom.: 36996

Bravo AF: 0.397

Asia WGS AF: 0.410 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.50
PhyloP100		0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12966547;

hg19: chr18-52752017;