chr13-42382485-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000637462.1(LINC02341):​n.230-1772C>T 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 0.0638 in 152,042 control chromosomes in the GnomAD database, including 334 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 0.064 ( 334 hom., cov: 32)

Consequence

LINC02341
ENST00000637462.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.148
Variant links:
Genes affected
LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02341ENST00000637462.1 linkuse as main transcriptn.230-1772C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0639
AC:
9702
AN:
151924
Hom.:
333
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0605
Gnomad AMI
AF:
0.0570
Gnomad AMR
AF:
0.0340
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.126
Gnomad SAS
AF:
0.134
Gnomad FIN
AF:
0.103
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.0532
Gnomad OTH
AF:
0.0574
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0638
AC:
9703
AN:
152042
Hom.:
334
Cov.:
32
AF XY:
0.0691
AC XY:
5131
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.0604
Gnomad4 AMR
AF:
0.0340
Gnomad4 ASJ
AF:
0.134
Gnomad4 EAS
AF:
0.127
Gnomad4 SAS
AF:
0.133
Gnomad4 FIN
AF:
0.103
Gnomad4 NFE
AF:
0.0532
Gnomad4 OTH
AF:
0.0577
Alfa
AF:
0.0565
Hom.:
347
Bravo
AF:
0.0555
Asia WGS
AF:
0.117
AC:
409
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.0
DANN
Benign
0.58

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17638544; hg19: chr13-42956621; API