13-42443364-G-C

Variant names:

• chr13-42443364-G-C
• rs1324005
• ENST00000637043.2:n.336+5892G>C

Variant summary

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

The ENST00000637043.2(LINC02341):​n.336+5892G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,128 control chromosomes in the GnomAD database, including 2,786 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 0.17 (2786 hom., cov: 32)
• Consequence: LINC02341 ENST00000637043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 7 publications found

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637043.2. 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
	LINC02341	NR_135319.1		n.336+5892G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637043.2	TSL:3	n.336+5892G>C		intron	N/A
	LINC02341	ENST00000637462.1	TSL:5	n.1118-603G>C		intron	N/A
	LINC02341	ENST00000765075.1		n.349-603G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26573 AN: 152010 Hom.: 2778 Cov.: 32

Gnomad AFR AF: 0.0694

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.175 AC: 26583 AN: 152128 Hom.: 2786 Cov.: 32 AF XY: 0.173 AC XY: 12829 AN XY: 74370

African (AFR) AF: 0.0694 AC: 2882 AN: 41538

American (AMR) AF: 0.151 AC: 2304 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3470

East Asian (EAS) AF: 0.171 AC: 887 AN: 5178

South Asian (SAS) AF: 0.297 AC: 1430 AN: 4818

European-Finnish (FIN) AF: 0.177 AC: 1870 AN: 10574

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15516 AN: 67968

Other (OTH) AF: 0.188 AC: 395 AN: 2106

Alfa AF: 0.107 Hom.: 187

Bravo AF: 0.166

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.52
DANN	Benign	0.36
PhyloP100		-0.27

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1324005;

hg19: chr13-43017500;