chr2-209693307-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001375505.1(MAP2):c.1137G>A(p.Met379Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,613,800 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_001375505.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2 | NM_001375505.1 | c.1137G>A | p.Met379Ile | missense_variant | 8/16 | ENST00000682079.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2 | ENST00000682079.1 | c.1137G>A | p.Met379Ile | missense_variant | 8/16 | NM_001375505.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250114Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135288
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461662Hom.: 0 Cov.: 34 AF XY: 0.00000550 AC XY: 4AN XY: 727118
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2023 | The c.1137G>A (p.M379I) alteration is located in exon 7 (coding exon 4) of the MAP2 gene. This alteration results from a G to A substitution at nucleotide position 1137, causing the methionine (M) at amino acid position 379 to be replaced by an isoleucine (I). 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