13-42358789-G-A

Position:

• chr13-42358789-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637462.1(LINC02341):​n.229+16187G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,874 control chromosomes in the GnomAD database, including 12,840 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 0.40 (12840 hom., cov: 31)
• Consequence: LINC02341 ENST00000637462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02341	ENST00000637462.1	n.229+16187G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61191 AN: 151756 Hom.: 12826 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.403 AC: 61248 AN: 151874 Hom.: 12840 Cov.: 31 AF XY: 0.407 AC XY: 30208 AN XY: 74228

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.443

Alfa AF: 0.388 Hom.: 21983

Bravo AF: 0.419

Asia WGS AF: 0.520 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs238270; hg19: chr13-42932925;