Variant rs3862138 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002373.6(MAP1A):c.2328C>T(p.Pro776Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 1,613,830 control chromosomes in the GnomAD database, including 28,835 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2359 hom., cov: 32)

Exomes 𝑓: 0.18 ( 26476 hom. )

Consequence

MAP1A
NM_002373.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.193

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP7

Synonymous conserved (PhyloP=-0.193 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 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.2328C>T	p.Pro776Pro	synonymous_variant	4/6	ENST00000300231.6	NP_002364.5	P78559-1Q504X9
MAP1A	NM_001411089.1 linkuse as main transcript	c.3042C>T	p.Pro1014Pro	synonymous_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.2328C>T	p.Pro776Pro	synonymous_variant	4/6	5	NM_002373.6	ENSP00000300231.5		P78559-1
MAP1A	ENST00000382031.5 linkuse as main transcript	c.3042C>T	p.Pro1014Pro	synonymous_variant	5/7	5		ENSP00000371462.1		E9PGC8

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25867

AN:

152030

Hom.:

2362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.185

GnomAD3 exomes

AF:

0.161

AC:

40045

AN:

248040

Hom.:

3699

AF XY:

0.168

AC XY:

22664

AN XY:

134772

show subpopulations

Gnomad AFR exome

AF:

0.172

Gnomad AMR exome

AF:

0.103

Gnomad ASJ exome

AF:

0.214

Gnomad EAS exome

AF:

0.00251

Gnomad SAS exome

AF:

0.207

Gnomad FIN exome

AF:

0.130

Gnomad NFE exome

AF:

0.191

Gnomad OTH exome

AF:

0.179

GnomAD4 exome

AF:

0.184

AC:

269073

AN:

1461680

Hom.:

26476

Cov.:

AF XY:

0.186

AC XY:

134978

AN XY:

727128

show subpopulations

Gnomad4 AFR exome

AF:

0.172

Gnomad4 AMR exome

AF:

0.108

Gnomad4 ASJ exome

AF:

0.214

Gnomad4 EAS exome

AF:

0.00146

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.131

Gnomad4 NFE exome

AF:

0.193

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.170

AC:

25875

AN:

152150

Hom.:

2359

Cov.:

AF XY:

0.166

AC XY:

12377

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.172

Gnomad4 AMR

AF:

0.146

Gnomad4 ASJ

AF:

0.215

Gnomad4 EAS

AF:

0.00154

Gnomad4 SAS

AF:

0.186

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.190

Gnomad4 OTH

AF:

0.183

Alfa

AF:

0.191

Hom.:

1541

Bravo

AF:

0.170

Asia WGS

AF:

0.0840

AC:

296

AN:

3476

EpiCase

AF:

0.196

EpiControl

AF:

0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

8.2

DANN

Benign

0.60

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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