13-105758919-T-A

Variant names:

• chr13-105758919-T-A
• rs9514424
• ENST00000415294.3:n.887-2344T>A

Variant summary

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

The ENST00000415294.3(LINC00343):​n.887-2344T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,996 control chromosomes in the GnomAD database, including 20,505 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 0.50 (20505 hom., cov: 31)
• Consequence: LINC00343 ENST00000415294.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 2 publications found

Genes affected

LINC00343 (HGNC:42500): (long intergenic non-protein coding RNA 343)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00343	NR_046391.2	n.743-2344T>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00343	ENST00000415294.3	n.887-2344T>A		intron_variant	Intron 3 of 4	5
LINC00343	ENST00000454555.2	n.928-2344T>A		intron_variant	Intron 3 of 3	2
LINC00343	ENST00000598229.2	n.195-2344T>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76106 AN: 151878 Hom.: 20491 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.501 AC: 76144 AN: 151996 Hom.: 20505 Cov.: 31 AF XY: 0.510 AC XY: 37903 AN XY: 74274

African (AFR) AF: 0.296 AC: 12278 AN: 41438

American (AMR) AF: 0.595 AC: 9085 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1910 AN: 3466

East Asian (EAS) AF: 0.730 AC: 3766 AN: 5162

South Asian (SAS) AF: 0.567 AC: 2735 AN: 4826

European-Finnish (FIN) AF: 0.683 AC: 7214 AN: 10564

Middle Eastern (MID) AF: 0.451 AC: 130 AN: 288

European-Non Finnish (NFE) AF: 0.551 AC: 37438 AN: 67964

Other (OTH) AF: 0.509 AC: 1073 AN: 2106

Alfa AF: 0.520 Hom.: 2663

Bravo AF: 0.488

Asia WGS AF: 0.630 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	4.2
DANN	Benign	0.89
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs9514424; hg19: chr13-106411268;