13-42440328-G-A

Variant names:

• chr13-42440328-G-A
• rs12864265
• ENST00000637043.2:n.336+2856G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000637043.2(LINC02341):​n.336+2856G>A 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 152,202 control chromosomes in the GnomAD database, including 2,790 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 (2790 hom., cov: 32)
• Consequence: LINC02341 ENST00000637043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• 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+2856G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637043.2	TSL:3	n.336+2856G>A		intron	N/A
	LINC02341	ENST00000637462.1	TSL:5	n.1117+2856G>A		intron	N/A
	LINC02341	ENST00000765075.1		n.348+2856G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26587 AN: 152084 Hom.: 2782 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.175 AC: 26597 AN: 152202 Hom.: 2790 Cov.: 32 AF XY: 0.173 AC XY: 12841 AN XY: 74402

African (AFR) AF: 0.0693 AC: 2877 AN: 41536

American (AMR) AF: 0.151 AC: 2309 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3472

East Asian (EAS) AF: 0.171 AC: 886 AN: 5178

South Asian (SAS) AF: 0.296 AC: 1431 AN: 4828

European-Finnish (FIN) AF: 0.177 AC: 1872 AN: 10588

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

European-Non Finnish (NFE) AF: 0.228 AC: 15524 AN: 67986

Other (OTH) AF: 0.188 AC: 397 AN: 2114

Alfa AF: 0.120 Hom.: 305

Bravo AF: 0.166

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	9.8
DANN	Benign	0.67
PhyloP100		0.070

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: rs12864265;

hg19: chr13-43014464;