10-70352092-C-T

Variant summary

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

The NM_001278212.2(LRRC20):​c.83-11390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 151,996 control chromosomes in the GnomAD database, including 42,858 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 0.75 ( 42858 hom., cov: 31)

Consequence

LRRC20
NM_001278212.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.317

Publications

10 publications found
Variant links:
Genes affected
LRRC20 (HGNC:23421): (leucine rich repeat containing 20)

Genome browser will be placed here

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=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LRRC20NM_001278212.2 linkc.83-11390G>A intron_variant Intron 2 of 4 ENST00000446961.4 NP_001265141.1 Q8TCA0-1A0A024QZM2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LRRC20ENST00000446961.4 linkc.83-11390G>A intron_variant Intron 2 of 4 2 NM_001278212.2 ENSP00000413745.2 Q8TCA0-1X6RK58

Frequencies

GnomAD3 genomes
AF:
0.748
AC:
113552
AN:
151878
Hom.:
42809
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.678
Gnomad AMI
AF:
0.817
Gnomad AMR
AF:
0.800
Gnomad ASJ
AF:
0.773
Gnomad EAS
AF:
0.661
Gnomad SAS
AF:
0.566
Gnomad FIN
AF:
0.805
Gnomad MID
AF:
0.823
Gnomad NFE
AF:
0.785
Gnomad OTH
AF:
0.784
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.748
AC:
113648
AN:
151996
Hom.:
42858
Cov.:
31
AF XY:
0.749
AC XY:
55688
AN XY:
74306
show subpopulations
African (AFR)
AF:
0.678
AC:
28082
AN:
41422
American (AMR)
AF:
0.801
AC:
12227
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.773
AC:
2683
AN:
3470
East Asian (EAS)
AF:
0.660
AC:
3412
AN:
5168
South Asian (SAS)
AF:
0.567
AC:
2735
AN:
4820
European-Finnish (FIN)
AF:
0.805
AC:
8478
AN:
10538
Middle Eastern (MID)
AF:
0.833
AC:
245
AN:
294
European-Non Finnish (NFE)
AF:
0.785
AC:
53383
AN:
67990
Other (OTH)
AF:
0.786
AC:
1658
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1417
2834
4252
5669
7086
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
844
1688
2532
3376
4220
<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:
0.770
Hom.:
165861
Bravo
AF:
0.746
Asia WGS
AF:
0.598
AC:
2079
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
0.80
DANN
Benign
0.30
PhyloP100
0.32
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: rs10509322; hg19: chr10-72111848; COSMIC: COSV62939542; API