4-155355865-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039580.2(MAP9):c.1141T>A(p.Leu381Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,613,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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.1141T>A | p.Leu381Met | missense_variant | 9/14 | ENST00000311277.9 | |
MAP9-AS1 | NR_125937.1 | n.159-1224A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP9 | ENST00000311277.9 | c.1141T>A | p.Leu381Met | missense_variant | 9/14 | 1 | NM_001039580.2 | P1 | |
MAP9-AS1 | ENST00000630664.2 | n.374-1224A>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000560 AC: 14AN: 250026Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135248
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1460806Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 726748
GnomAD4 genome ? AF: 0.000243 AC: 37AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.1141T>A (p.L381M) alteration is located in exon 9 (coding exon 8) of the MAP9 gene. This alteration results from a T to A substitution at nucleotide position 1141, causing the leucine (L) at amino acid position 381 to be replaced by a methionine (M). 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