chr10-46550349-T-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001385282.1(GPRIN2):c.388A>T(p.Met130Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 7/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 75)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GPRIN2
NM_001385282.1 missense
NM_001385282.1 missense
Scores
8
Clinical Significance
Conservation
PhyloP100: 0.954
Genes affected
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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=0.11379808).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPRIN2 | NM_001385282.1 | c.388A>T | p.Met130Leu | missense_variant | 3/3 | ENST00000374314.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPRIN2 | ENST00000374314.6 | c.388A>T | p.Met130Leu | missense_variant | 3/3 | NM_001385282.1 | P1 | ||
GPRIN2 | ENST00000374317.2 | c.388A>T | p.Met130Leu | missense_variant | 3/3 | 3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 75
GnomAD3 genomes
Cov.:
75
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1460646Hom.: 0 Cov.: 114 AF XY: 0.00 AC XY: 0AN XY: 726642
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1460646
Hom.:
Cov.:
114
AF XY:
AC XY:
0
AN XY:
726642
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 75
GnomAD4 genome
Cov.:
75
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 | Mar 07, 2023 | The c.388A>T (p.M130L) alteration is located in exon 3 (coding exon 1) of the GPRIN2 gene. This alteration results from a A to T substitution at nucleotide position 388, causing the methionine (M) at amino acid position 130 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
Benign
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
MetaRNN
Benign
T;T
PROVEAN
Benign
N;N
Sift
Benign
T;T
Sift4G
Benign
T;T
Vest4
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at