rs60502351

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000438867.1(LINC01283):​n.71-395C>A 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 0.00925 in 112,093 control chromosomes in the GnomAD database, including 8 homozygotes. There are 265 hemizygotes in GnomAD. 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 0.0093 ( 8 hom., 265 hem., cov: 23)

Consequence

LINC01283
ENST00000438867.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.225
Variant links:
Genes affected
LINC01283 (HGNC:50339): (long intergenic non-protein coding RNA 1283)

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).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00925 (1037/112093) while in subpopulation AFR AF= 0.0321 (988/30808). AF 95% confidence interval is 0.0304. There are 8 homozygotes in gnomad4. There are 265 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC01283ENST00000438867.1 linkuse as main transcriptn.71-395C>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.00920
AC:
1031
AN:
112040
Hom.:
8
Cov.:
23
AF XY:
0.00760
AC XY:
260
AN XY:
34216
show subpopulations
Gnomad AFR
AF:
0.0319
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00338
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000564
Gnomad OTH
AF:
0.00730
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00925
AC:
1037
AN:
112093
Hom.:
8
Cov.:
23
AF XY:
0.00773
AC XY:
265
AN XY:
34279
show subpopulations
Gnomad4 AFR
AF:
0.0321
Gnomad4 AMR
AF:
0.00328
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000564
Gnomad4 OTH
AF:
0.00721
Alfa
AF:
0.0112
Hom.:
21
Bravo
AF:
0.0108

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.26
DANN
Benign
0.37

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: rs60502351; hg19: chrX-39263534; API