2-100221105-T-C

Variant summary

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

The NR_103730.1(LINC01104):​n.567+12285T>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 0.546 in 152,092 control chromosomes in the GnomAD database, including 23,336 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 0.55 ( 23336 hom., cov: 32)

Consequence

LINC01104
NR_103730.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.94
Variant links:
Genes affected
LINC01104 (HGNC:49226): (long intergenic non-protein coding RNA 1104)

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=-1.04).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC01104NR_103730.1 linkuse as main transcriptn.567+12285T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC01104ENST00000452354.5 linkuse as main transcriptn.567+12285T>C intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.546
AC:
82967
AN:
151974
Hom.:
23321
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.445
Gnomad AMI
AF:
0.509
Gnomad AMR
AF:
0.454
Gnomad ASJ
AF:
0.601
Gnomad EAS
AF:
0.609
Gnomad SAS
AF:
0.477
Gnomad FIN
AF:
0.677
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.605
Gnomad OTH
AF:
0.530
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.546
AC:
83027
AN:
152092
Hom.:
23336
Cov.:
32
AF XY:
0.547
AC XY:
40686
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.445
Gnomad4 AMR
AF:
0.454
Gnomad4 ASJ
AF:
0.601
Gnomad4 EAS
AF:
0.609
Gnomad4 SAS
AF:
0.478
Gnomad4 FIN
AF:
0.677
Gnomad4 NFE
AF:
0.606
Gnomad4 OTH
AF:
0.529
Alfa
AF:
0.579
Hom.:
8959
Bravo
AF:
0.526
Asia WGS
AF:
0.497
AC:
1731
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.022
DANN
Benign
0.41

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: rs2309837; hg19: chr2-100837567; API