13-42346024-G-A

Variant names:

• chr13-42346024-G-A
• rs430586
• ENST00000637462.1:n.229+3422G>A

Variant summary

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

The ENST00000637462.1(LINC02341):​n.229+3422G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,942 control chromosomes in the GnomAD database, including 22,783 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 0.54 (22783 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637462.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637462.1	TSL:5	n.229+3422G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82739 AN: 151824 Hom.: 22770 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.545 AC: 82795 AN: 151942 Hom.: 22783 Cov.: 32 AF XY: 0.546 AC XY: 40511 AN XY: 74248

African (AFR) AF: 0.602 AC: 24934 AN: 41438

American (AMR) AF: 0.542 AC: 8270 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2253 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3371 AN: 5166

South Asian (SAS) AF: 0.533 AC: 2564 AN: 4814

European-Finnish (FIN) AF: 0.488 AC: 5136 AN: 10522

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34485 AN: 67950

Other (OTH) AF: 0.565 AC: 1195 AN: 2114

Alfa AF: 0.528 Hom.: 3727

Bravo AF: 0.553

Asia WGS AF: 0.563 AC: 1955 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.84
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs430586; hg19: chr13-42920160;