chr4-155362134-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039580.2(MAP9):c.716G>A(p.Cys239Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000166 in 1,565,400 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001039580.2 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 |
---|---|---|---|---|---|---|---|
MAP9 | NM_001039580.2 | c.716G>A | p.Cys239Tyr | missense_variant | 6/14 | ENST00000311277.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP9 | ENST00000311277.9 | c.716G>A | p.Cys239Tyr | missense_variant | 6/14 | 1 | NM_001039580.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151906Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000141 AC: 3AN: 212806Hom.: 0 AF XY: 0.0000259 AC XY: 3AN XY: 115904
GnomAD4 exome AF: 0.0000177 AC: 25AN: 1413494Hom.: 0 Cov.: 27 AF XY: 0.0000213 AC XY: 15AN XY: 703142
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151906Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74174
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.716G>A (p.C239Y) alteration is located in exon 6 (coding exon 5) of the MAP9 gene. This alteration results from a G to A substitution at nucleotide position 716, causing the cysteine (C) at amino acid position 239 to be replaced by a tyrosine (Y). 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