13-42444041-A-T

Position:

• chr13-42444041-A-T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.1192A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,172 control chromosomes in the GnomAD database, including 48,414 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 0.80 (48414 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC02341 ENST00000637462.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02341	NR_135319.1	n.336+6569A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02341	ENST00000637462.1	n.1192A>T		non_coding_transcript_exon_variant	8/8	5
LINC02341	ENST00000637043.1	n.336+6569A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121111 AN: 152054 Hom.: 48364 Cov.: 32

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.797

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.797 AC: 121211 AN: 152172 Hom.: 48414 Cov.: 32 AF XY: 0.799 AC XY: 59466 AN XY: 74408

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.794

Alfa AF: 0.785 Hom.: 5485

Bravo AF: 0.801

Asia WGS AF: 0.742 AC: 2580 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720824; hg19: chr13-43018177;