chr6-159036117-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_054114.5(TAGAP):c.1906C>G(p.Pro636Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,613,716 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_054114.5 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 |
---|---|---|---|---|---|---|---|
TAGAP | NM_054114.5 | c.1906C>G | p.Pro636Ala | missense_variant | 10/10 | ENST00000367066.8 | |
TAGAP-AS1 | NR_183546.1 | n.701-4802G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAGAP | ENST00000367066.8 | c.1906C>G | p.Pro636Ala | missense_variant | 10/10 | 1 | NM_054114.5 | P1 | |
TAGAP-AS1 | ENST00000646912.1 | n.26-5681G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152046Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 251086Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135688
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461552Hom.: 1 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727020
GnomAD4 genome ? AF: 0.0000986 AC: 15AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2022 | The c.1906C>G (p.P636A) alteration is located in exon 10 (coding exon 9) of the TAGAP gene. This alteration results from a C to G substitution at nucleotide position 1906, causing the proline (P) at amino acid position 636 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