rs2062305

Variant names:

• chr13-42478744-G-A
• rs2062305
• ENST00000637043.2:n.337-6725G>A

Variant summary

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

The ENST00000637043.2(LINC02341):​n.337-6725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,124 control chromosomes in the GnomAD database, including 16,535 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 0.45 (16535 hom., cov: 33)
• Consequence: LINC02341 ENST00000637043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.76
• Publications: 46 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 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.337-6725G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637043.2	TSL:3	n.337-6725G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69102 AN: 152006 Hom.: 16532 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.454 AC: 69121 AN: 152124 Hom.: 16535 Cov.: 33 AF XY: 0.457 AC XY: 34019 AN XY: 74382

African (AFR) AF: 0.343 AC: 14225 AN: 41496

American (AMR) AF: 0.422 AC: 6443 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5164

South Asian (SAS) AF: 0.458 AC: 2209 AN: 4824

European-Finnish (FIN) AF: 0.617 AC: 6527 AN: 10578

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35663 AN: 67992

Other (OTH) AF: 0.447 AC: 943 AN: 2110

Alfa AF: 0.481 Hom.: 25988

Bravo AF: 0.434

Asia WGS AF: 0.327 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs2062305; hg19: chr13-43052880;