6-136491177-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MAP7	NM_003980.6	c.67+59165A>G		intron_variant		ENST00000354570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP7	ENST00000354570.8	c.67+59165A>G		intron_variant		1	NM_003980.6	A2

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

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.713

Alfa AF: 0.786 Hom.: 72993

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

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

Other links and lift over

dbSNP: rs2181096; hg19: chr6-136812315;