Genetic Variant MAP7:c.68-62845G>A (chr6-136484644-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003980.6(MAP7):c.68-62845G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,016 control chromosomes in the GnomAD database, including 13,333 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 0.34 ( 13333 hom., cov: 32)

Consequence

MAP7
NM_003980.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.906

Publications

1 publications found

Variant links:

Genes affected

MAP7 (HGNC:6869): (microtubule associated protein 7) The product of this gene is a microtubule-associated protein that is predominantly expressed in cells of epithelial origin. Microtubule-associated proteins are thought to be involved in microtubule dynamics, which is essential for cell polarization and differentiation. This protein has been shown to be able to stabilize microtubules, and may serve to modulate microtubule functions. Studies of the related mouse protein also suggested an essential role in microtubule function required for spermatogenesis. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]

MAP7 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003980.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAP7	NM_003980.6	MANE Select	c.68-62845G>A	intron	N/A	NP_003971.1	Q14244-1
MAP7	NM_001198609.2		c.133+41188G>A	intron	N/A	NP_001185538.1	A0A087WZ40
MAP7	NM_001388328.1		c.133+41188G>A	intron	N/A	NP_001375257.1	A0A087WZ40

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAP7	ENST00000354570.8	TSL:1 MANE Select	c.68-62845G>A	intron	N/A	ENSP00000346581.2	Q14244-1
MAP7	ENST00000617204.4	TSL:2	c.133+41188G>A	intron	N/A	ENSP00000482335.1	A0A087WZ40
MAP7	ENST00000877105.1		c.68-62845G>A	intron	N/A	ENSP00000547164.1

Frequencies

GnomAD3 genomes

AF:

0.339

AC:

51559

AN:

151898

Hom.:

13286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.724

Gnomad AMI

AF:

0.295

Gnomad AMR

AF:

0.285

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.309

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.340

AC:

51673

AN:

152016

Hom.:

13333

Cov.:

AF XY:

0.334

AC XY:

24822

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.724

AC:

30016

AN:

41448

American (AMR)

AF:

0.285

AC:

4350

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.166

AC:

577

AN:

3470

East Asian (EAS)

AF:

0.409

AC:

2120

AN:

5178

South Asian (SAS)

AF:

0.158

AC:

758

AN:

4802

European-Finnish (FIN)

AF:

0.151

AC:

1591

AN:

10566

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11277

AN:

67962

Other (OTH)

AF:

0.313

AC:

660

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1289

2577

3866

5154

6443

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

438

876

1314

1752

2190

<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:

0.267

Hom.:

1411

Bravo

AF:

0.369

Asia WGS

AF:

0.332

AC:

1154

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.71

(source)

DANN

Benign

0.34

PhyloP100

-0.91

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over