13-105796582-A-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667534.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00343	ENST00000667534.1		n.849A>C		non_coding_transcript_exon	Exon 3 of 3
	LINC00343	ENST00000669840.1		n.1410A>C		non_coding_transcript_exon	Exon 2 of 2
	LINC00343	ENST00000831894.1		n.848A>C		non_coding_transcript_exon	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

African (AFR) AF: 0.0960 AC: 3987 AN: 41544

American (AMR) AF: 0.214 AC: 3260 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3470

East Asian (EAS) AF: 0.138 AC: 712 AN: 5162

South Asian (SAS) AF: 0.154 AC: 744 AN: 4818

European-Finnish (FIN) AF: 0.0905 AC: 959 AN: 10596

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7497 AN: 68000

Other (OTH) AF: 0.135 AC: 286 AN: 2114

Alfa AF: 0.113 Hom.: 1682

Bravo AF: 0.127

Asia WGS AF: 0.125 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.42
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2149144; hg19: chr13-106448931;