dbSNP rs16843614: MAP2:c.*203G>A (chr2-209730600-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001375505.1(MAP2):c.*203G>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.101 in 566,952 control chromosomes in the GnomAD database, including 3,845 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 0.12 ( 1398 hom., cov: 32)

Exomes 𝑓: 0.094 ( 2447 hom. )

Consequence

MAP2
NM_001375505.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.94

Publications

8 publications found

Variant links:

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]

MAP2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375505.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MAP2	NM_001375505.1	MANE Select	c.*203G>A	3_prime_UTR	Exon 16 of 16	NP_001362434.1
MAP2	NR_164694.1		n.1522G>A	non_coding_transcript_exon	Exon 9 of 9
MAP2	NR_164695.1		n.1540G>A	non_coding_transcript_exon	Exon 9 of 9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MAP2	ENST00000682079.1	MANE Select	c.*203G>A	3_prime_UTR	Exon 16 of 16	ENSP00000507035.1
MAP2	ENST00000392194.5	TSL:1	c.*203G>A	3_prime_UTR	Exon 11 of 11	ENSP00000376032.1
MAP2	ENST00000673860.1		c.*203G>A	3_prime_UTR	Exon 17 of 17	ENSP00000501117.1

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18086

AN:

152018

Hom.:

1395

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.0549

Gnomad AMR

AF:

0.0819

Gnomad ASJ

AF:

0.109

Gnomad EAS

AF:

0.226

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.0805

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0689

Gnomad OTH

AF:

0.106

GnomAD4 exome

AF:

0.0940

AC:

38978

AN:

414816

Hom.:

2447

Cov.:

AF XY:

0.0957

AC XY:

20903

AN XY:

218330

show subpopulations

African (AFR)

AF:

0.218

AC:

2561

AN:

11746

American (AMR)

AF:

0.0717

AC:

1257

AN:

17540

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

1281

AN:

12628

East Asian (EAS)

AF:

0.224

AC:

6308

AN:

28118

South Asian (SAS)

AF:

0.144

AC:

6045

AN:

42124

European-Finnish (FIN)

AF:

0.0817

AC:

2141

AN:

26208

Middle Eastern (MID)

AF:

0.119

AC:

213

AN:

1792

European-Non Finnish (NFE)

AF:

0.0674

AC:

16885

AN:

250510

Other (OTH)

AF:

0.0947

AC:

2287

AN:

24150

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1578

3156

4734

6312

7890

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

194

388

582

776

970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.119

AC:

18109

AN:

152136

Hom.:

1398

Cov.:

AF XY:

0.120

AC XY:

8940

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.211

AC:

8729

AN:

41464

American (AMR)

AF:

0.0825

AC:

1262

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.109

AC:

377

AN:

3470

East Asian (EAS)

AF:

0.226

AC:

1166

AN:

5170

South Asian (SAS)

AF:

0.150

AC:

725

AN:

4818

European-Finnish (FIN)

AF:

0.0805

AC:

853

AN:

10594

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0689

AC:

4688

AN:

68008

Other (OTH)

AF:

0.105

AC:

223

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

783

1566

2349

3132

3915

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0825

Hom.:

885

Bravo

AF:

0.121

Asia WGS

AF:

0.180

AC:

623

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

3.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over