13-34572478-T-G

Variant names:

• chr13-34572478-T-G
• rs1344431
• ENST00000791012.1:n.796T>G

Variant summary

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

The ENST00000791012.1(LINC02343):​n.796T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,044 control chromosomes in the GnomAD database, including 25,312 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 0.57 (25312 hom., cov: 33)
• Consequence: LINC02343 ENST00000791012.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 4 publications found

Genes affected

LINC02343 (HGNC:53263): (long intergenic non-protein coding RNA 2343)

LINC00457 (HGNC:42805): (long intergenic non-protein coding RNA 457)

ENSG00000271901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00457	NR_047036.1	n.82-38073A>C		intron_variant	Intron 1 of 2
LINC02343	NR_146542.1	n.171-35998T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02343	ENST00000791012.1	n.796T>G		non_coding_transcript_exon_variant	Exon 4 of 4
LINC02343	ENST00000791013.1	n.851T>G		non_coding_transcript_exon_variant	Exon 5 of 5
LINC00457	ENST00000440160.1	n.82-38073A>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86815 AN: 151926 Hom.: 25306 Cov.: 33

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.571 AC: 86845 AN: 152044 Hom.: 25312 Cov.: 33 AF XY: 0.576 AC XY: 42837 AN XY: 74316

African (AFR) AF: 0.464 AC: 19233 AN: 41446

American (AMR) AF: 0.632 AC: 9655 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1871 AN: 3466

East Asian (EAS) AF: 0.839 AC: 4342 AN: 5174

South Asian (SAS) AF: 0.630 AC: 3040 AN: 4828

European-Finnish (FIN) AF: 0.604 AC: 6381 AN: 10558

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40327 AN: 67974

Other (OTH) AF: 0.594 AC: 1253 AN: 2108

Alfa AF: 0.588 Hom.: 98637

Bravo AF: 0.573

Asia WGS AF: 0.710 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1344431; hg19: chr13-35146615;