chr13-42344512-C-T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.229+1910C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,068 control chromosomes in the GnomAD database, including 5,799 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 0.27 ( 5799 hom., cov: 32)

Consequence

LINC02341
ENST00000637462.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.141
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 (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02341ENST00000637462.1 linkn.229+1910C>T intron_variant Intron 2 of 7 5

Frequencies

GnomAD3 genomes
AF:
0.274
AC:
41625
AN:
151950
Hom.:
5796
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.296
Gnomad AMI
AF:
0.342
Gnomad AMR
AF:
0.221
Gnomad ASJ
AF:
0.228
Gnomad EAS
AF:
0.137
Gnomad SAS
AF:
0.269
Gnomad FIN
AF:
0.308
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.280
Gnomad OTH
AF:
0.267
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.274
AC:
41651
AN:
152068
Hom.:
5799
Cov.:
32
AF XY:
0.270
AC XY:
20062
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.296
Gnomad4 AMR
AF:
0.221
Gnomad4 ASJ
AF:
0.228
Gnomad4 EAS
AF:
0.137
Gnomad4 SAS
AF:
0.268
Gnomad4 FIN
AF:
0.308
Gnomad4 NFE
AF:
0.280
Gnomad4 OTH
AF:
0.269
Alfa
AF:
0.279
Hom.:
2940
Bravo
AF:
0.267
Asia WGS
AF:
0.209
AC:
728
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
3.4
DANN
Benign
0.47

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: rs9525613; hg19: chr13-42918648; API