chr6-136471826-C-G

Variant summary

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

The NM_003980.6(MAP7):​c.68-50027G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,078 control chromosomes in the GnomAD database, including 43,362 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 0.74 ( 43362 hom., cov: 32)

Consequence

MAP7
NM_003980.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0390
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]

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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 (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MAP7NM_003980.6 linkuse as main transcriptc.68-50027G>C intron_variant ENST00000354570.8 NP_003971.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MAP7ENST00000354570.8 linkuse as main transcriptc.68-50027G>C intron_variant 1 NM_003980.6 ENSP00000346581 A2Q14244-1

Frequencies

GnomAD3 genomes
AF:
0.745
AC:
113229
AN:
151960
Hom.:
43360
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.572
Gnomad AMI
AF:
0.706
Gnomad AMR
AF:
0.751
Gnomad ASJ
AF:
0.834
Gnomad EAS
AF:
0.556
Gnomad SAS
AF:
0.841
Gnomad FIN
AF:
0.847
Gnomad MID
AF:
0.845
Gnomad NFE
AF:
0.836
Gnomad OTH
AF:
0.750
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.745
AC:
113259
AN:
152078
Hom.:
43362
Cov.:
32
AF XY:
0.747
AC XY:
55564
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.571
Gnomad4 AMR
AF:
0.752
Gnomad4 ASJ
AF:
0.834
Gnomad4 EAS
AF:
0.556
Gnomad4 SAS
AF:
0.841
Gnomad4 FIN
AF:
0.847
Gnomad4 NFE
AF:
0.836
Gnomad4 OTH
AF:
0.746
Alfa
AF:
0.785
Hom.:
5633
Bravo
AF:
0.728
Asia WGS
AF:
0.671
AC:
2336
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
2.7
DANN
Benign
0.38

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.

Other links and lift over

dbSNP: rs720565; hg19: chr6-136792964; API