chr4-151701366-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004564.3(GATB):c.1160A>T(p.Gln387Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000264 in 1,589,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004564.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATB | NM_004564.3 | c.1160A>T | p.Gln387Leu | missense_variant | 9/13 | ENST00000263985.11 | |
GATB | NM_001363341.2 | c.1160A>T | p.Gln387Leu | missense_variant | 9/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATB | ENST00000263985.11 | c.1160A>T | p.Gln387Leu | missense_variant | 9/13 | 1 | NM_004564.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000344 AC: 8AN: 232688Hom.: 0 AF XY: 0.0000159 AC XY: 2AN XY: 126054
GnomAD4 exome AF: 0.0000146 AC: 21AN: 1437060Hom.: 0 Cov.: 31 AF XY: 0.0000140 AC XY: 10AN XY: 714458
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.1160A>T (p.Q387L) alteration is located in exon 9 (coding exon 9) of the GATB gene. This alteration results from a A to T substitution at nucleotide position 1160, causing the glutamine (Q) at amino acid position 387 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at