13-60878379-G-C

Variant summary

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

The ENST00000658247.1(LINC00378):​n.363+27853G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,174 control chromosomes in the GnomAD database, including 58,448 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 0.88 ( 58448 hom., cov: 32)

Consequence

LINC00378
ENST00000658247.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.328
Variant links:
Genes affected
LINC00378 (HGNC:42704): (long intergenic non-protein coding RNA 378)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
LINC00378ENST00000658247.1 linkn.363+27853G>C intron_variant Intron 3 of 4

Frequencies

GnomAD3 genomes
AF:
0.876
AC:
133183
AN:
152056
Hom.:
58405
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.857
Gnomad AMI
AF:
0.866
Gnomad AMR
AF:
0.909
Gnomad ASJ
AF:
0.909
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.896
Gnomad FIN
AF:
0.901
Gnomad MID
AF:
0.854
Gnomad NFE
AF:
0.863
Gnomad OTH
AF:
0.881
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.876
AC:
133281
AN:
152174
Hom.:
58448
Cov.:
32
AF XY:
0.879
AC XY:
65357
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.857
Gnomad4 AMR
AF:
0.910
Gnomad4 ASJ
AF:
0.909
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.896
Gnomad4 FIN
AF:
0.901
Gnomad4 NFE
AF:
0.863
Gnomad4 OTH
AF:
0.883
Alfa
AF:
0.844
Hom.:
2655
Bravo
AF:
0.877
Asia WGS
AF:
0.949
AC:
3298
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.92
DANN
Benign
0.45

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: rs301653; hg19: chr13-61452513; API