chr17-46546274-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_001006607.3(LRRC37A2):c.3073G>A(p.Ala1025Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00084 ( 0 hom., cov: 21)
Exomes 𝑓: 0.000097 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LRRC37A2
NM_001006607.3 missense
NM_001006607.3 missense
Scores
4
10
Clinical Significance
Conservation
PhyloP100: 0.235
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]
Genome browser will be placed here
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=0.010158032).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A2 | NM_001006607.3 | c.3073G>A | p.Ala1025Thr | missense_variant | 8/14 | ENST00000576629.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A2 | ENST00000576629.6 | c.3073G>A | p.Ala1025Thr | missense_variant | 8/14 | 5 | NM_001006607.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 108AN: 128940Hom.: 0 Cov.: 21 FAILED QC
GnomAD3 genomes
?
AF:
AC:
108
AN:
128940
Hom.:
Cov.:
21
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000967 AC: 59AN: 609938Hom.: 0 Cov.: 8 AF XY: 0.0000971 AC XY: 32AN XY: 329416
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
59
AN:
609938
Hom.:
Cov.:
8
AF XY:
AC XY:
32
AN XY:
329416
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
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.000845 AC: 109AN: 129032Hom.: 0 Cov.: 21 AF XY: 0.000917 AC XY: 57AN XY: 62148
GnomAD4 genome
?
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
109
AN:
129032
Hom.:
Cov.:
21
AF XY:
AC XY:
57
AN XY:
62148
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ExAC
?
AF:
AC:
3
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 | Nov 05, 2021 | The c.3073G>A (p.A1025T) alteration is located in exon 8 (coding exon 8) of the LRRC37A2 gene. This alteration results from a G to A substitution at nucleotide position 3073, causing the alanine (A) at amino acid position 1025 to be replaced by a threonine (T). 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
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D;D;N;N
PrimateAI
Uncertain
T
Sift4G
Uncertain
D;D
Polyphen
B;B
Vest4
MutPred
Gain of loop (P = 0.2045);Gain of loop (P = 0.2045);
MVP
ClinPred
T
GERP RS
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