rs2149144

chr13-105796582-A-Cchr13-105796582-A-G

Variant summary

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

The ENST00000669840.1(LINC00343):n.1410A>C 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 0.119 in 152,176 control chromosomes in the GnomAD database, including 1,242 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 0.12 (1242 hom., cov: 33)
• Consequence: LINC00343 ENST00000669840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00343	ENST00000669840.1	n.1410A>C		non_coding_transcript_exon_variant	2/2
LINC00343	ENST00000667534.1	n.849A>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18070 AN: 152058 Hom.: 1230 Cov.: 33

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.119 AC: 18112 AN: 152176 Hom.: 1242 Cov.: 33 AF XY: 0.119 AC XY: 8850 AN XY: 74398

Gnomad4 AFR AF: 0.0960

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0905

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.135

Alfa AF: 0.110 Hom.: 1265

Bravo AF: 0.127

Asia WGS AF: 0.125 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.34
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2149144; hg19: chr13-106448931;