4-131565033-T-C

Variant summary

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

The NR_183920.1(LINC02377):​n.784+95410T>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 0.157 in 152,136 control chromosomes in the GnomAD database, including 2,131 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 0.16 ( 2131 hom., cov: 32)

Consequence

LINC02377
NR_183920.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.127
Variant links:
Genes affected
LINC02377 (HGNC:53300): (long intergenic non-protein coding RNA 2377)

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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02377NR_183920.1 linkuse as main transcriptn.784+95410T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02377ENST00000654488.1 linkuse as main transcriptn.849-26237T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.158
AC:
23968
AN:
152018
Hom.:
2131
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0941
Gnomad AMI
AF:
0.231
Gnomad AMR
AF:
0.141
Gnomad ASJ
AF:
0.199
Gnomad EAS
AF:
0.0195
Gnomad SAS
AF:
0.0755
Gnomad FIN
AF:
0.207
Gnomad MID
AF:
0.231
Gnomad NFE
AF:
0.205
Gnomad OTH
AF:
0.169
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.157
AC:
23960
AN:
152136
Hom.:
2131
Cov.:
32
AF XY:
0.156
AC XY:
11568
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.0938
Gnomad4 AMR
AF:
0.141
Gnomad4 ASJ
AF:
0.199
Gnomad4 EAS
AF:
0.0197
Gnomad4 SAS
AF:
0.0764
Gnomad4 FIN
AF:
0.207
Gnomad4 NFE
AF:
0.205
Gnomad4 OTH
AF:
0.167
Alfa
AF:
0.138
Hom.:
342
Bravo
AF:
0.150
Asia WGS
AF:
0.0630
AC:
219
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
4.4
DANN
Benign
0.65

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: rs350961; hg19: chr4-132486188; API