chr5-154891467-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015465.5(GEMIN5):āc.4036A>Gā(p.Thr1346Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000837 in 1,613,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015465.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GEMIN5 | NM_015465.5 | c.4036A>G | p.Thr1346Ala | missense_variant | 26/28 | ENST00000285873.8 | |
GEMIN5 | NM_001252156.2 | c.4033A>G | p.Thr1345Ala | missense_variant | 26/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GEMIN5 | ENST00000285873.8 | c.4036A>G | p.Thr1346Ala | missense_variant | 26/28 | 1 | NM_015465.5 | P1 | |
GEMIN5 | ENST00000522075.1 | n.540A>G | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251174Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135724
GnomAD4 exome AF: 0.0000896 AC: 131AN: 1461406Hom.: 0 Cov.: 33 AF XY: 0.0000935 AC XY: 68AN XY: 727036
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2022 | The c.4036A>G (p.T1346A) alteration is located in exon 26 (coding exon 26) of the GEMIN5 gene. This alteration results from a A to G substitution at nucleotide position 4036, causing the threonine (T) at amino acid position 1346 to be replaced by an alanine (A). 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