rs2149144

Variant names:

• chr13-105796582-A-C
• rs2149144
• ENST00000667534.1:n.849A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-105796582-A-C
• chr13-105796582-A-G

Variant summary

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

The ENST00000667534.1(LINC00343):​n.849A>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 ENST00000667534.1 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00343	ENST00000667534.1	n.849A>C		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00343	ENST00000669840.1	n.1410A>C		non_coding_transcript_exon_variant	Exon 2 of 2

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;