18-55083238-A-G

Variant names:

• chr18-55083238-A-G
• rs4309482
• ENST00000774238.1:n.317-34650A>G

Variant summary

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

The ENST00000774238.1(ENSG00000300819):​n.317-34650A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,958 control chromosomes in the GnomAD database, including 12,008 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 0.40 (12008 hom., cov: 31)
• Consequence: ENSG00000300819 ENST00000774238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 15 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300819	ENST00000774238.1		n.317-34650A>G		intron	N/A
	ENSG00000300838	ENST00000774358.1		n.449+3660T>C		intron	N/A
	ENSG00000300838	ENST00000774359.1		n.138-3958T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60083 AN: 151840 Hom.: 11999 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.396 AC: 60123 AN: 151958 Hom.: 12008 Cov.: 31 AF XY: 0.396 AC XY: 29385 AN XY: 74252

African (AFR) AF: 0.352 AC: 14604 AN: 41450

American (AMR) AF: 0.407 AC: 6199 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3472

East Asian (EAS) AF: 0.610 AC: 3147 AN: 5160

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4816

European-Finnish (FIN) AF: 0.436 AC: 4604 AN: 10558

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27465 AN: 67950

Other (OTH) AF: 0.382 AC: 805 AN: 2108

Alfa AF: 0.404 Hom.: 41592

Bravo AF: 0.400

Asia WGS AF: 0.414 AC: 1439 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4309482; hg19: chr18-52750469;