6-136491177-T-C

Variant names:

• chr6-136491177-T-C
• rs2181096
• NM_003980.6:c.67+59165A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003980.6(MAP7):​c.67+59165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,056 control chromosomes in the GnomAD database, including 38,813 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 0.70 (38813 hom., cov: 32)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 2 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP7	NM_003980.6	c.67+59165A>G		intron_variant	Intron 1 of 17	ENST00000354570.8	NP_003971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP7	ENST00000354570.8	c.67+59165A>G		intron_variant	Intron 1 of 17	1	NM_003980.6	ENSP00000346581.2

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106104 AN: 151938 Hom.: 38817 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.698 AC: 106129 AN: 152056 Hom.: 38813 Cov.: 32 AF XY: 0.703 AC XY: 52273 AN XY: 74318

African (AFR) AF: 0.469 AC: 19426 AN: 41444

American (AMR) AF: 0.725 AC: 11073 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2813 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3055 AN: 5170

South Asian (SAS) AF: 0.840 AC: 4052 AN: 4824

European-Finnish (FIN) AF: 0.829 AC: 8760 AN: 10564

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54582 AN: 68000

Other (OTH) AF: 0.713 AC: 1508 AN: 2114

Alfa AF: 0.769 Hom.: 168371

Bravo AF: 0.677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.99
DANN	Benign	0.70
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2181096; hg19: chr6-136812315;