chr17-74737037-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The XR_007065905.1(LOC124904057):n.82+221C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,607,364 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: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
LOC124904057
XR_007065905.1 intron, non_coding_transcript
XR_007065905.1 intron, non_coding_transcript
Scores
1
2
12
Clinical Significance
Conservation
PhyloP100: 0.198
Genes affected
RAB37 (HGNC:30268): (RAB37, member RAS oncogene family) Rab proteins are low molecular mass GTPases that are critical regulators of vesicle trafficking. For additional background information on Rab proteins, see MIM 179508.[supplied by OMIM, Apr 2006]
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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=0.18206811).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124904057 | XR_007065905.1 | n.82+221C>T | intron_variant, non_coding_transcript_variant | ||||
RAB37 | NM_001163989.3 | c.-84G>A | 5_prime_UTR_variant | 1/9 | |||
RAB37 | NM_001330471.2 | c.12+306G>A | intron_variant | ||||
RAB37 | NM_175738.5 | c.184-5217G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB37 | ENST00000392614.8 | c.-84G>A | 5_prime_UTR_variant | 1/9 | 2 | P2 | |||
RAB37 | ENST00000392615.9 | c.-291G>A | 5_prime_UTR_variant | 1/8 | 3 | ||||
RAB37 | ENST00000340415.7 | c.184-5217G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000216 AC: 5AN: 231904Hom.: 0 AF XY: 0.0000234 AC XY: 3AN XY: 128020
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GnomAD4 exome AF: 0.0000117 AC: 17AN: 1455172Hom.: 0 Cov.: 32 AF XY: 0.0000111 AC XY: 8AN XY: 723706
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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 | Oct 26, 2022 | The c.28G>A (p.A10T) alteration is located in exon 1 (coding exon 1) of the RAB37 gene. This alteration results from a G to A substitution at nucleotide position 28, causing the alanine (A) at amino acid position 10 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
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Pathogenic
D;D
Polyphen
B;.
Vest4
MutPred
Gain of phosphorylation at A10 (P = 0.0417);Gain of phosphorylation at A10 (P = 0.0417);
MVP
MPC
0.18
ClinPred
D
GERP RS
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