rs997139

Positions:

• chr6-136429980-G-A
• chr6-136429980-G-T

Variant summary

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

The NM_003980.6(MAP7):​c.68-8181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,068 control chromosomes in the GnomAD database, including 43,282 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 0.75 (43282 hom., cov: 32)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.908

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP7	NM_003980.6	c.68-8181C>T		intron_variant		ENST00000354570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP7	ENST00000354570.8	c.68-8181C>T		intron_variant		1	NM_003980.6	A2

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113397 AN: 151950 Hom.: 43279 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.746 AC: 113427 AN: 152068 Hom.: 43282 Cov.: 32 AF XY: 0.749 AC XY: 55688 AN XY: 74332

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.751

Alfa AF: 0.813 Hom.: 47705

Bravo AF: 0.729

Asia WGS AF: 0.672 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.44

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: rs997139; hg19: chr6-136751118;