rs948426

Variant summary

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

The NR_120518.1(LINC01387):​n.284-8807A>G 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 0.299 in 152,082 control chromosomes in the GnomAD database, including 8,782 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 0.30 ( 8782 hom., cov: 32)

Consequence

LINC01387
NR_120518.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.149
Variant links:
Genes affected
LINC01387 (HGNC:44660): (long intergenic non-protein coding RNA 1387)

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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC01387NR_120518.1 linkuse as main transcriptn.284-8807A>G intron_variant, non_coding_transcript_variant
LOC105371972XR_935116.4 linkuse as main transcriptn.1022-1350A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000582386.3 linkuse as main transcriptn.674-1350A>G intron_variant, non_coding_transcript_variant 3
LINC01387ENST00000584361.1 linkuse as main transcriptn.284-8807A>G intron_variant, non_coding_transcript_variant 3
ENST00000684855.1 linkuse as main transcriptn.386-1350A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.299
AC:
45470
AN:
151964
Hom.:
8786
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0744
Gnomad AMI
AF:
0.436
Gnomad AMR
AF:
0.309
Gnomad ASJ
AF:
0.293
Gnomad EAS
AF:
0.0684
Gnomad SAS
AF:
0.351
Gnomad FIN
AF:
0.487
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.419
Gnomad OTH
AF:
0.281
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.299
AC:
45466
AN:
152082
Hom.:
8782
Cov.:
32
AF XY:
0.300
AC XY:
22329
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.0743
Gnomad4 AMR
AF:
0.309
Gnomad4 ASJ
AF:
0.293
Gnomad4 EAS
AF:
0.0686
Gnomad4 SAS
AF:
0.351
Gnomad4 FIN
AF:
0.487
Gnomad4 NFE
AF:
0.419
Gnomad4 OTH
AF:
0.277
Alfa
AF:
0.383
Hom.:
15293
Bravo
AF:
0.274
Asia WGS
AF:
0.192
AC:
670
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.6
DANN
Benign
0.53

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: rs948426; hg19: chr18-6567182; API