NM_003980.6:c.67+53992T>C

Variant names:

• chr6-136496350-A-G
• rs9399183
• NM_003980.6:c.67+53992T>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.67+53992T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,092 control chromosomes in the GnomAD database, including 13,416 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 (13416 hom., cov: 32)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP7	NM_003980.6	c.67+53992T>C		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+53992T>C		intron_variant	Intron 1 of 17	1	NM_003980.6	ENSP00000346581.2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51679 AN: 151974 Hom.: 13369 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.341 AC: 51793 AN: 152092 Hom.: 13416 Cov.: 32 AF XY: 0.335 AC XY: 24886 AN XY: 74358

African (AFR) AF: 0.726 AC: 30091 AN: 41476

American (AMR) AF: 0.286 AC: 4375 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 573 AN: 3460

East Asian (EAS) AF: 0.411 AC: 2119 AN: 5154

South Asian (SAS) AF: 0.159 AC: 769 AN: 4828

European-Finnish (FIN) AF: 0.150 AC: 1586 AN: 10600

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11292 AN: 67968

Other (OTH) AF: 0.315 AC: 665 AN: 2114

Alfa AF: 0.233 Hom.: 7821

Bravo AF: 0.370

Asia WGS AF: 0.336 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.76
PhyloP100		-0.49
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: rs9399183; hg19: chr6-136817488;