chr7-150337409-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142928.2(LRRC61):c.548T>C(p.Leu183Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,453,396 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
LRRC61
NM_001142928.2 missense
NM_001142928.2 missense
Scores
6
12
Clinical Significance
Conservation
PhyloP100: 1.26
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.10516137).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC61 | NM_001142928.2 | c.548T>C | p.Leu183Ser | missense_variant | 3/3 | ENST00000359623.9 | |
LRRC61 | NM_001363433.1 | c.548T>C | p.Leu183Ser | missense_variant | 3/3 | ||
LRRC61 | NM_001363434.1 | c.548T>C | p.Leu183Ser | missense_variant | 3/3 | ||
LRRC61 | NM_023942.3 | c.548T>C | p.Leu183Ser | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC61 | ENST00000359623.9 | c.548T>C | p.Leu183Ser | missense_variant | 3/3 | 2 | NM_001142928.2 | P1 | |
LRRC61 | ENST00000323078.7 | c.548T>C | p.Leu183Ser | missense_variant | 2/2 | 1 | P1 | ||
LRRC61 | ENST00000493307.1 | c.548T>C | p.Leu183Ser | missense_variant | 4/4 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1453396Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 2AN XY: 723454
GnomAD4 exome
AF:
AC:
2
AN:
1453396
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
723454
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
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Gnomad4 OTH exome
AF:
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
Bravo
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2022 | The c.548T>C (p.L183S) alteration is located in exon 3 (coding exon 1) of the LRRC61 gene. This alteration results from a T to C substitution at nucleotide position 548, causing the leucine (L) at amino acid position 183 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M
MutationTaster
Benign
N;N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
B;B;B
Vest4
MutPred
Gain of phosphorylation at L183 (P = 0.0068);Gain of phosphorylation at L183 (P = 0.0068);Gain of phosphorylation at L183 (P = 0.0068);
MVP
MPC
0.28
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at