rs12876893

Variant names:

• chr13-30828694-G-A
• rs12876893
• ENST00000715721.1:n.708+15021G>A

Variant summary

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

The ENST00000715721.1(LINC00398):​n.708+15021G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,978 control chromosomes in the GnomAD database, including 8,530 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 0.31 (8530 hom., cov: 31)
• Consequence: LINC00398 ENST00000715721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 4 publications found

Genes affected

LINC00398 (HGNC:42727): (long intergenic non-protein coding RNA 398)

ENSG00000304203 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00398	ENST00000715721.1	n.708+15021G>A		intron_variant	Intron 3 of 3
ENSG00000304203	ENST00000801014.1	n.344-2491C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47672 AN: 151860 Hom.: 8529 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.314 AC: 47697 AN: 151978 Hom.: 8530 Cov.: 31 AF XY: 0.321 AC XY: 23866 AN XY: 74278

African (AFR) AF: 0.154 AC: 6375 AN: 41470

American (AMR) AF: 0.407 AC: 6211 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1094 AN: 3464

East Asian (EAS) AF: 0.530 AC: 2734 AN: 5156

South Asian (SAS) AF: 0.527 AC: 2531 AN: 4804

European-Finnish (FIN) AF: 0.375 AC: 3959 AN: 10562

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23708 AN: 67956

Other (OTH) AF: 0.332 AC: 699 AN: 2108

Alfa AF: 0.346 Hom.: 13601

Bravo AF: 0.309

Asia WGS AF: 0.496 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.38
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs12876893; hg19: chr13-31402831;