13-60885853-C-T

Variant summary

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

The ENST00000658247.1(LINC00378):​n.363+35327C>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 0.891 in 152,146 control chromosomes in the GnomAD database, including 60,451 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 0.89 ( 60451 hom., cov: 32)

Consequence

LINC00378
ENST00000658247.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.23
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
LINC00378ENST00000658247.1 linkuse as main transcriptn.363+35327C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.891
AC:
135437
AN:
152028
Hom.:
60415
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.861
Gnomad AMI
AF:
0.870
Gnomad AMR
AF:
0.929
Gnomad ASJ
AF:
0.934
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.900
Gnomad FIN
AF:
0.902
Gnomad MID
AF:
0.905
Gnomad NFE
AF:
0.887
Gnomad OTH
AF:
0.909
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.891
AC:
135528
AN:
152146
Hom.:
60451
Cov.:
32
AF XY:
0.892
AC XY:
66351
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.861
Gnomad4 AMR
AF:
0.929
Gnomad4 ASJ
AF:
0.934
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
0.899
Gnomad4 FIN
AF:
0.902
Gnomad4 NFE
AF:
0.887
Gnomad4 OTH
AF:
0.911
Alfa
AF:
0.886
Hom.:
6972
Bravo
AF:
0.893
Asia WGS
AF:
0.950
AC:
3301
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
0.060
DANN
Benign
0.44

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: rs301640; hg19: chr13-61459987; API