chr2-209693389-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001375505.1(MAP2):c.1219G>T(p.Val407Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000722 in 1,612,078 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0040 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00038 ( 0 hom. )
Consequence
MAP2
NM_001375505.1 missense
NM_001375505.1 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 2.15
Genes affected
MAP2 (HGNC:6839): (microtubule associated protein 2) This gene encodes a protein that belongs to the microtubule-associated protein family. The proteins of this family are thought to be involved in microtubule assembly, which is an essential step in neurogenesis. The products of similar genes in rat and mouse are neuron-specific cytoskeletal proteins that are enriched in dentrites, implicating a role in determining and stabilizing dentritic shape during neuron development. A number of alternatively spliced variants encoding distinct isoforms have been described. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0044187307).
BP6
?
Variant 2-209693389-G-T is Benign according to our data. Variant chr2-209693389-G-T is described in ClinVar as [Benign]. Clinvar id is 791122.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 600 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2 | NM_001375505.1 | c.1219G>T | p.Val407Phe | missense_variant | 8/16 | ENST00000682079.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2 | ENST00000682079.1 | c.1219G>T | p.Val407Phe | missense_variant | 8/16 | NM_001375505.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00394 AC: 600AN: 152136Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.000973 AC: 242AN: 248610Hom.: 2 AF XY: 0.000677 AC XY: 91AN XY: 134364
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GnomAD4 exome AF: 0.000384 AC: 561AN: 1459824Hom.: 0 Cov.: 34 AF XY: 0.000314 AC XY: 228AN XY: 726204
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GnomAD4 genome ? AF: 0.00396 AC: 603AN: 152254Hom.: 6 Cov.: 32 AF XY: 0.00400 AC XY: 298AN XY: 74458
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Benign
T;T;T
Polyphen
P;.;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at