chr13-42478744-G-A

Position:

• chr13-42478744-G-A

Variant summary

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

The NR_135319.1(LINC02341):​n.337-6725G>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 0.454 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 NR_135319.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.76

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02341	NR_135319.1	n.337-6725G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02341	ENST00000637043.1	n.337-6725G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.447

Alfa AF: 0.490 Hom.: 14565

Bravo AF: 0.434

Asia WGS AF: 0.327 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2062305; hg19: chr13-43052880;