rs9399183

chr6-136496350-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• 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/exons	MANE	UniProt
MAP7	NM_003980.6	c.67+53992T>C		intron_variant		ENST00000354570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP7	ENST00000354570.8	c.67+53992T>C		intron_variant		1	NM_003980.6	A2

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

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.315

Alfa AF: 0.210 Hom.: 4599

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

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: rs9399183; hg19: chr6-136817488;