Variant rs2245715 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002373.6(MAP1A):c.4381G>A(p.Asp1461Asn) variant causes a missense change. The variant allele was found at a frequency of 0.147 in 1,610,258 control chromosomes in the GnomAD database, including 30,066 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.27 ( 9125 hom., cov: 32)

Exomes 𝑓: 0.13 ( 20941 hom. )

Consequence

MAP1A
NM_002373.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.80

Variant links:

Genes affected

MAP1A (HGNC:6835): (microtubule associated protein 1A) 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 product of this gene is a precursor polypeptide that presumably undergoes proteolytic processing to generate the final MAP1A heavy chain and LC2 light chain. Expression of this gene is almost exclusively in the brain. Studies of the rat microtubule-associated protein 1A gene suggested a role in early events of spinal cord development. [provided by RefSeq, Jul 2008]

MAP1A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.7787941E-5).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP1A	NM_002373.6 linkuse as main transcript	c.4381G>A	p.Asp1461Asn	missense_variant	4/6	ENST00000300231.6	NP_002364.5
MAP1A	NM_001411089.1 linkuse as main transcript	c.5095G>A	p.Asp1699Asn	missense_variant	5/7		NP_001398018.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP1A	ENST00000300231.6 linkuse as main transcript	c.4381G>A	p.Asp1461Asn	missense_variant	4/6	5	NM_002373.6	ENSP00000300231	P2	P78559-1
MAP1A	ENST00000382031.5 linkuse as main transcript	c.5095G>A	p.Asp1699Asn	missense_variant	5/7	5		ENSP00000371462	A2

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40459

AN:

151832

Hom.:

9103

Cov.:

show subpopulations

Gnomad AFR

AF:

0.609

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.188

Gnomad EAS

AF:

0.432

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.0798

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.0982

Gnomad OTH

AF:

0.230

GnomAD3 exomes

AF:

0.190

AC:

47158

AN:

248060

Hom.:

7230

AF XY:

0.181

AC XY:

24397

AN XY:

134840

show subpopulations

Gnomad AFR exome

AF:

0.619

Gnomad AMR exome

AF:

0.212

Gnomad ASJ exome

AF:

0.194

Gnomad EAS exome

AF:

0.448

Gnomad SAS exome

AF:

0.214

Gnomad FIN exome

AF:

0.0755

Gnomad NFE exome

AF:

0.101

Gnomad OTH exome

AF:

0.150

GnomAD4 exome

AF:

0.134

AC:

195669

AN:

1458308

Hom.:

20941

Cov.:

AF XY:

0.135

AC XY:

97754

AN XY:

725366

show subpopulations

Gnomad4 AFR exome

AF:

0.636

Gnomad4 AMR exome

AF:

0.209

Gnomad4 ASJ exome

AF:

0.193

Gnomad4 EAS exome

AF:

0.433

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.0761

Gnomad4 NFE exome

AF:

0.0991

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.267

AC:

40535

AN:

151950

Hom.:

9125

Cov.:

AF XY:

0.264

AC XY:

19594

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.609

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.188

Gnomad4 EAS

AF:

0.431

Gnomad4 SAS

AF:

0.227

Gnomad4 FIN

AF:

0.0798

Gnomad4 NFE

AF:

0.0982

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.138

Hom.:

4247

Bravo

AF:

0.298

TwinsUK

AF:

0.0952

AC:

353

ALSPAC

AF:

0.108

AC:

417

ESP6500AA

AF:

0.589

AC:

2194

ESP6500EA

AF:

0.102

AC:

839

ExAC

AF:

0.195

AC:

23595

Asia WGS

AF:

0.349

AC:

1213

AN:

3478

EpiCase

AF:

0.111

EpiControl

AF:

0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.098

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.041

.;T

Eigen

Benign

-0.59

Eigen_PC

Benign

-0.63

FATHMM_MKL

Benign

0.17

LIST_S2

Benign

0.79

T;T

MetaRNN

Benign

0.000018

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.6

.;M

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.24

PROVEAN

Benign

-0.35

N;N

REVEL

Benign

0.097

Sift

Benign

0.088

T;T

Sift4G

Benign

0.35

T;T

Polyphen

0.14

.;B

Vest4

0.042

MPC

0.53

ClinPred

0.036

GERP RS

3.0

Varity_R

0.078

gMVP

0.018

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over