chr2-209693410-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.1240G>T(p.Ala414Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00836 in 1,613,134 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0073 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0085 ( 76 hom. )
Consequence
MAP2
NM_001375505.1 missense
NM_001375505.1 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 0.989
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0036669672).
BP6
?
Variant 2-209693410-G-T is Benign according to our data. Variant chr2-209693410-G-T is described in ClinVar as [Benign]. Clinvar id is 778822.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 1115 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2 | NM_001375505.1 | c.1240G>T | p.Ala414Ser | missense_variant | 8/16 | ENST00000682079.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2 | ENST00000682079.1 | c.1240G>T | p.Ala414Ser | missense_variant | 8/16 | NM_001375505.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00733 AC: 1115AN: 152096Hom.: 4 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1115
AN:
152096
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00719 AC: 1794AN: 249652Hom.: 14 AF XY: 0.00720 AC XY: 972AN XY: 134936
GnomAD3 exomes
AF:
AC:
1794
AN:
249652
Hom.:
AF XY:
AC XY:
972
AN XY:
134936
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00847 AC: 12369AN: 1460920Hom.: 76 Cov.: 34 AF XY: 0.00835 AC XY: 6067AN XY: 726776
GnomAD4 exome
AF:
AC:
12369
AN:
1460920
Hom.:
Cov.:
34
AF XY:
AC XY:
6067
AN XY:
726776
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00732 AC: 1114AN: 152214Hom.: 4 Cov.: 32 AF XY: 0.00750 AC XY: 558AN XY: 74428
GnomAD4 genome
?
AF:
AC:
1114
AN:
152214
Hom.:
Cov.:
32
AF XY:
AC XY:
558
AN XY:
74428
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
30
ALSPAC
AF:
AC:
34
ESP6500AA
AF:
AC:
6
ESP6500EA
AF:
AC:
68
ExAC
?
AF:
AC:
856
Asia WGS
AF:
AC:
2
AN:
3478
EpiCase
AF:
EpiControl
AF:
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
Benign
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;T;D
Sift4G
Benign
T;T;T
Polyphen
B;.;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at