ENST00000774238.1:n.317-34431T>G

Variant names:

• chr18-55083457-T-G
• rs11874716
• ENST00000774238.1:n.317-34431T>G

Variant summary

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

The ENST00000774238.1(ENSG00000300819):​n.317-34431T>G 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 151,908 control chromosomes in the GnomAD database, including 11,906 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 (11906 hom., cov: 32)
• Consequence: ENSG00000300819 ENST00000774238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 17 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03035	XR_935478.3	n.772+1364A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300819	ENST00000774238.1	n.317-34431T>G		intron_variant	Intron 1 of 1
ENSG00000300838	ENST00000774358.1	n.449+3441A>C		intron_variant	Intron 2 of 2
ENSG00000300838	ENST00000774359.1	n.138-4177A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59803 AN: 151790 Hom.: 11897 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.394 AC: 59842 AN: 151908 Hom.: 11906 Cov.: 32 AF XY: 0.394 AC XY: 29245 AN XY: 74248

African (AFR) AF: 0.345 AC: 14306 AN: 41416

American (AMR) AF: 0.407 AC: 6210 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1289 AN: 3462

East Asian (EAS) AF: 0.607 AC: 3131 AN: 5154

South Asian (SAS) AF: 0.288 AC: 1384 AN: 4806

European-Finnish (FIN) AF: 0.437 AC: 4614 AN: 10554

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

European-Non Finnish (NFE) AF: 0.404 AC: 27478 AN: 67934

Other (OTH) AF: 0.381 AC: 806 AN: 2116

Alfa AF: 0.402 Hom.: 19814

Bravo AF: 0.397

Asia WGS AF: 0.411 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11874716; hg19: chr18-52750688;