GeneBe

chr4-17990709-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001394446.1(LCORL):​c.155-17824T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 149,120 control chromosomes in the GnomAD database, including 5,834 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 0.25 ( 5834 hom., cov: 28)

Consequence

LCORL
NM_001394446.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

4 publications found
Variant links:
Genes affected
LCORL (HGNC:30776): (ligand dependent nuclear receptor corepressor like) This gene encodes a transcription factor that appears to function in spermatogenesis. Polymorphisms in this gene are associated with measures of skeletal frame size and adult height. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LCORLNM_001394446.1 linkc.155-17824T>C intron_variant Intron 1 of 7 ENST00000635767.2 NP_001381375.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LCORLENST00000635767.2 linkc.155-17824T>C intron_variant Intron 1 of 7 5 NM_001394446.1 ENSP00000490600.1 A0A1B0GVP4

Frequencies

GnomAD3 genomes
AF:
0.245
AC:
36502
AN:
149022
Hom.:
5805
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.453
Gnomad AMI
AF:
0.242
Gnomad AMR
AF:
0.200
Gnomad ASJ
AF:
0.282
Gnomad EAS
AF:
0.138
Gnomad SAS
AF:
0.278
Gnomad FIN
AF:
0.0921
Gnomad MID
AF:
0.197
Gnomad NFE
AF:
0.158
Gnomad OTH
AF:
0.239
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
36570
AN:
149120
Hom.:
5834
Cov.:
28
AF XY:
0.242
AC XY:
17538
AN XY:
72476
show subpopulations
African (AFR)
AF:
0.454
AC:
18234
AN:
40196
American (AMR)
AF:
0.200
AC:
2984
AN:
14910
Ashkenazi Jewish (ASJ)
AF:
0.282
AC:
973
AN:
3452
East Asian (EAS)
AF:
0.138
AC:
696
AN:
5058
South Asian (SAS)
AF:
0.278
AC:
1302
AN:
4684
European-Finnish (FIN)
AF:
0.0921
AC:
911
AN:
9892
Middle Eastern (MID)
AF:
0.205
AC:
59
AN:
288
European-Non Finnish (NFE)
AF:
0.158
AC:
10696
AN:
67658
Other (OTH)
AF:
0.239
AC:
496
AN:
2078
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
1152
2304
3456
4608
5760
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
362
724
1086
1448
1810
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.208
Hom.:
6182
Bravo
AF:
0.260
Asia WGS
AF:
0.242
AC:
843
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
0.74
DANN
Benign
0.67
PhyloP100
-1.1
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs16896210; hg19: chr4-17992332; API