6-136547791-G-A

Position:

• chr6-136547791-G-A

Variant summary

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

The NM_003980.6(MAP7):​c.67+2551C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,768 control chromosomes in the GnomAD database, including 5,981 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 0.25 (5981 hom., cov: 32)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP7	NM_003980.6	c.67+2551C>T		intron_variant		ENST00000354570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP7	ENST00000354570.8	c.67+2551C>T		intron_variant		1	NM_003980.6	A2
MAP7	ENST00000616617.4	c.67+2551C>T		intron_variant		5		A2
MAP7	ENST00000618822.4	c.67+2551C>T		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38272 AN: 151650 Hom.: 5955 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.253 AC: 38355 AN: 151768 Hom.: 5981 Cov.: 32 AF XY: 0.249 AC XY: 18478 AN XY: 74152

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.250

Alfa AF: 0.180 Hom.: 1312

Bravo AF: 0.269

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.65

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: rs3799472; hg19: chr6-136868929;