rs7338389

Variant names:

• chr13-46520002-C-T
• rs7338389
• ENST00000781180.1:n.421+14234G>A

Variant summary

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

The ENST00000781180.1(LINC01198):​n.421+14234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,118 control chromosomes in the GnomAD database, including 23,849 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 0.51 (23849 hom., cov: 32)
• Consequence: LINC01198 ENST00000781180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 4 publications found

Genes affected

LINC01198 (HGNC:49598): (long intergenic non-protein coding RNA 1198) Biomarker of malignant astrocytoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000781180.1. 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
	LINC01198	ENST00000781180.1		n.421+14234G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77560 AN: 152000 Hom.: 23812 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.510 AC: 77635 AN: 152118 Hom.: 23849 Cov.: 32 AF XY: 0.504 AC XY: 37476 AN XY: 74376

African (AFR) AF: 0.866 AC: 35942 AN: 41504

American (AMR) AF: 0.472 AC: 7209 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1702 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2750 AN: 5170

South Asian (SAS) AF: 0.369 AC: 1780 AN: 4820

European-Finnish (FIN) AF: 0.244 AC: 2587 AN: 10594

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24157 AN: 67972

Other (OTH) AF: 0.508 AC: 1073 AN: 2114

Alfa AF: 0.407 Hom.: 59997

Bravo AF: 0.546

Asia WGS AF: 0.456 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.96
DANN	Benign	0.65
PhyloP100		-0.42

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: rs7338389;

hg19: chr13-47094137;