NM_003980.6:c.877-1853T>C

Variant names:

• chr6-136368292-A-G
• rs2179288
• NM_003980.6:c.877-1853T>C

Variant summary

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

The NM_003980.6(MAP7):​c.877-1853T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 151,824 control chromosomes in the GnomAD database, including 44,722 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 0.76 (44722 hom., cov: 29)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.826 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP7	NM_003980.6	MANE Select	c.877-1853T>C		intron	N/A	NP_003971.1
	MAP7	NM_001198609.2		c.967-1853T>C		intron	N/A	NP_001185538.1
	MAP7	NM_001388328.1		c.967-1853T>C		intron	N/A	NP_001375257.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP7	ENST00000354570.8	TSL:1 MANE Select	c.877-1853T>C		intron	N/A	ENSP00000346581.2
	MAP7	ENST00000617204.4	TSL:2	c.967-1853T>C		intron	N/A	ENSP00000482335.1
	MAP7	ENST00000454590.5	TSL:2	c.943-1853T>C		intron	N/A	ENSP00000414712.1

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115377 AN: 151706 Hom.: 44704 Cov.: 29

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.760 AC: 115434 AN: 151824 Hom.: 44722 Cov.: 29 AF XY: 0.764 AC XY: 56713 AN XY: 74216

African (AFR) AF: 0.614 AC: 25383 AN: 41312

American (AMR) AF: 0.787 AC: 12010 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2888 AN: 3466

East Asian (EAS) AF: 0.613 AC: 3163 AN: 5162

South Asian (SAS) AF: 0.837 AC: 4025 AN: 4810

European-Finnish (FIN) AF: 0.853 AC: 9006 AN: 10560

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56510 AN: 67942

Other (OTH) AF: 0.766 AC: 1617 AN: 2112

Alfa AF: 0.788 Hom.: 5886

Bravo AF: 0.748

Asia WGS AF: 0.712 AC: 2479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-0.19
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: rs2179288; hg19: chr6-136689430;