chr17-46546292-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_001006607.3(LRRC37A2):c.3091T>C(p.Phe1031Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0018 ( 0 hom., cov: 20)
Exomes 𝑓: 0.00076 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LRRC37A2
NM_001006607.3 missense
NM_001006607.3 missense
Scores
2
3
9
Clinical Significance
Conservation
PhyloP100: -0.0430
Genes affected
LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
ARL17A (HGNC:24096): (ADP ribosylation factor like GTPase 17A) Predicted to enable GTP binding activity. Predicted to be involved in intracellular protein transport and vesicle-mediated transport. Predicted to be located in Golgi apparatus. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, LRRC37A2
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009926349).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A2 | NM_001006607.3 | c.3091T>C | p.Phe1031Leu | missense_variant | 8/14 | ENST00000576629.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A2 | ENST00000576629.6 | c.3091T>C | p.Phe1031Leu | missense_variant | 8/14 | 5 | NM_001006607.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 225AN: 128398Hom.: 0 Cov.: 20 FAILED QC
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128398
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20
FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000763 AC: 533AN: 698208Hom.: 0 Cov.: 9 AF XY: 0.000781 AC XY: 290AN XY: 371144
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00175 AC: 225AN: 128498Hom.: 0 Cov.: 20 AF XY: 0.00145 AC XY: 90AN XY: 61908
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?
Data not reliable, filtered out with message: AS_VQSR
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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 | Sep 01, 2021 | The c.3091T>C (p.F1031L) alteration is located in exon 8 (coding exon 8) of the LRRC37A2 gene. This alteration results from a T to C substitution at nucleotide position 3091, causing the phenylalanine (F) at amino acid position 1031 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M
MutationTaster
Benign
D;D;D;N;N
PrimateAI
Uncertain
T
Sift4G
Uncertain
T;T
Polyphen
P;P
Vest4
MutPred
Loss of methylation at K1032 (P = 0.0424);Loss of methylation at K1032 (P = 0.0424);
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at