chr4-155357501-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039580.2(MAP9):āc.1069A>Cā(p.Asn357His) variant causes a missense change. The variant allele was found at a frequency of 0.00000717 in 1,533,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N357K) has been classified 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.1069A>C | p.Asn357His | missense_variant | 8/14 | ENST00000311277.9 | |
MAP9-AS1 | NR_125937.1 | n.272+299T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP9 | ENST00000311277.9 | c.1069A>C | p.Asn357His | missense_variant | 8/14 | 1 | NM_001039580.2 | P1 | |
MAP9-AS1 | ENST00000630664.2 | n.487+299T>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249522Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134888
GnomAD4 exome AF: 0.00000434 AC: 6AN: 1381082Hom.: 0 Cov.: 23 AF XY: 0.00000145 AC XY: 1AN XY: 691596
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2024 | The c.1069A>C (p.N357H) alteration is located in exon 8 (coding exon 7) of the MAP9 gene. This alteration results from a A to C substitution at nucleotide position 1069, causing the asparagine (N) at amino acid position 357 to be replaced by a histidine (H). 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