rs3799419

chr6-136432080-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.68-10281A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,088 control chromosomes in the GnomAD database, including 7,335 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 0.28 (7335 hom., cov: 32)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP7	NM_003980.6	c.68-10281A>G		intron_variant		ENST00000354570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP7	ENST00000354570.8	c.68-10281A>G		intron_variant		1	NM_003980.6	A2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42914 AN: 151968 Hom.: 7327 Cov.: 32

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.282 AC: 42940 AN: 152088 Hom.: 7335 Cov.: 32 AF XY: 0.283 AC XY: 21055 AN XY: 74366

Gnomad4 AFR AF: 0.0786

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.299

Alfa AF: 0.359 Hom.: 13206

Bravo AF: 0.272

Asia WGS AF: 0.244 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.2
Dann	Benign	0.74

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: rs3799419; hg19: chr6-136753218; COSMIC: COSV63418422;