chr17-46297471-G-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_014834.4(LRRC37A):āc.2338G>Cā(p.Val780Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000060 ( 3 hom., cov: 18)
Exomes š: 0.00012 ( 40 hom. )
Failed GnomAD Quality Control
Consequence
LRRC37A
NM_014834.4 missense
NM_014834.4 missense
Scores
2
17
Clinical Significance
Conservation
PhyloP100: -0.200
Genes affected
LRRC37A (HGNC:29069): (leucine rich repeat containing 37A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
ARL17B (HGNC:32387): (ADP ribosylation factor like GTPase 17B) 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 -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0072587132).
BP6
Variant 17-46297471-G-C is Benign according to our data. Variant chr17-46297471-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3120581.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A | NM_014834.4 | c.2338G>C | p.Val780Leu | missense_variant | 1/14 | ENST00000320254.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A | ENST00000320254.5 | c.2338G>C | p.Val780Leu | missense_variant | 1/14 | 1 | NM_014834.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 9AN: 116400Hom.: 4 Cov.: 18 FAILED QC
GnomAD3 genomes
AF:
AC:
9
AN:
116400
Hom.:
Cov.:
18
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:
GnomAD3 exomes AF: 0.00129 AC: 65AN: 50466Hom.: 25 AF XY: 0.000943 AC XY: 24AN XY: 25444
GnomAD3 exomes
AF:
AC:
65
AN:
50466
Hom.:
AF XY:
AC XY:
24
AN XY:
25444
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000119 AC: 145AN: 1220840Hom.: 40 Cov.: 26 AF XY: 0.000110 AC XY: 68AN XY: 615498
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
145
AN:
1220840
Hom.:
Cov.:
26
AF XY:
AC XY:
68
AN XY:
615498
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: 0.0000601 AC: 7AN: 116486Hom.: 3 Cov.: 18 AF XY: 0.0000725 AC XY: 4AN XY: 55152
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
7
AN:
116486
Hom.:
Cov.:
18
AF XY:
AC XY:
4
AN XY:
55152
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.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.0
.;B
Vest4
MutPred
Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);
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