rs9514424

chr13-105758919-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046391.2(LINC00343):n.743-2344T>A variant causes a intron, non coding transcript 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 NR_046391.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00343	NR_046391.2	n.743-2344T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00343	ENST00000669840.1	n.224-36477T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.509

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9514424; hg19: chr13-106411268;