rs3799472

Variant names:

• chr6-136547791-G-A
• rs3799472
• NM_003980.6:c.67+2551C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MAP7	NM_003980.6	c.67+2551C>T		intron_variant	Intron 1 of 17	ENST00000354570.8	NP_003971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP7	ENST00000354570.8	c.67+2551C>T		intron_variant	Intron 1 of 17	1	NM_003980.6	ENSP00000346581.2
MAP7	ENST00000618822.4	c.67+2551C>T		intron_variant	Intron 1 of 16	5		ENSP00000482356.1
MAP7	ENST00000616617.4	c.67+2551C>T		intron_variant	Intron 1 of 15	5		ENSP00000483511.1

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

African (AFR) AF: 0.425 AC: 17574 AN: 41328

American (AMR) AF: 0.249 AC: 3794 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3456

East Asian (EAS) AF: 0.412 AC: 2125 AN: 5154

South Asian (SAS) AF: 0.153 AC: 732 AN: 4798

European-Finnish (FIN) AF: 0.150 AC: 1587 AN: 10550

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11132 AN: 67930

Other (OTH) AF: 0.250 AC: 527 AN: 2104

Alfa AF: 0.182 Hom.: 1533

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
PhyloP100		0.032
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3799472; hg19: chr6-136868929;