rs238272

Positions:

• chr13-42359719-T-C

Variant summary

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

The ENST00000637462.1(LINC02341):​n.229+17117T>C 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 0.702 in 152,116 control chromosomes in the GnomAD database, including 37,693 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 0.70 (37693 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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+17117T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106788 AN: 151998 Hom.: 37667 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.702 AC: 106861 AN: 152116 Hom.: 37693 Cov.: 33 AF XY: 0.707 AC XY: 52620 AN XY: 74396

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.721

Alfa AF: 0.699 Hom.: 3608

Bravo AF: 0.707

Asia WGS AF: 0.788 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs238272; hg19: chr13-42933855;