13-42346262-A-G

Variant names:

• chr13-42346262-A-G
• rs417768
• ENST00000637462.1:n.229+3660A>G

Variant summary

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

The ENST00000637462.1(LINC02341):​n.229+3660A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,098 control chromosomes in the GnomAD database, including 11,740 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 0.39 (11740 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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

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
	LINC02341	ENST00000637462.1	TSL:5	n.229+3660A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58617 AN: 151982 Hom.: 11730 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.386 AC: 58656 AN: 152098 Hom.: 11740 Cov.: 33 AF XY: 0.389 AC XY: 28928 AN XY: 74346

African (AFR) AF: 0.400 AC: 16617 AN: 41498

American (AMR) AF: 0.448 AC: 6841 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1928 AN: 3472

East Asian (EAS) AF: 0.605 AC: 3142 AN: 5190

South Asian (SAS) AF: 0.431 AC: 2071 AN: 4808

European-Finnish (FIN) AF: 0.274 AC: 2901 AN: 10570

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23869 AN: 67964

Other (OTH) AF: 0.419 AC: 882 AN: 2106

Alfa AF: 0.350 Hom.: 3383

Bravo AF: 0.402

Asia WGS AF: 0.475 AC: 1650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.49
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs417768; hg19: chr13-42920398;