rs720565

Positions:

• chr6-136471826-C-G
• chr6-136471826-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003980.6(MAP7):​c.68-50027G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,078 control chromosomes in the GnomAD database, including 43,362 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 0.74 (43362 hom., cov: 32)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP7	NM_003980.6	c.68-50027G>C		intron_variant		ENST00000354570.8	NP_003971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP7	ENST00000354570.8	c.68-50027G>C		intron_variant		1	NM_003980.6	ENSP00000346581	A2

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113229 AN: 151960 Hom.: 43360 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.745 AC: 113259 AN: 152078 Hom.: 43362 Cov.: 32 AF XY: 0.747 AC XY: 55564 AN XY: 74354

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.746

Alfa AF: 0.785 Hom.: 5633

Bravo AF: 0.728

Asia WGS AF: 0.671 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.38

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: rs720565; hg19: chr6-136792964;