chr2-74576549-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001321739.2(M1AP):c.839C>T(p.Ser280Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001321739.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
M1AP | NM_001321739.2 | c.839C>T | p.Ser280Phe | missense_variant | 6/11 | ENST00000421985.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
M1AP | ENST00000421985.2 | c.839C>T | p.Ser280Phe | missense_variant | 6/11 | 2 | NM_001321739.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251288Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135828
GnomAD4 exome AF: 0.000126 AC: 184AN: 1461782Hom.: 0 Cov.: 31 AF XY: 0.000109 AC XY: 79AN XY: 727202
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.839C>T (p.S280F) alteration is located in exon 6 (coding exon 5) of the M1AP gene. This alteration results from a C to T substitution at nucleotide position 839, causing the serine (S) at amino acid position 280 to be replaced by a phenylalanine (F). 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