rs3799419

Variant names:

• chr6-136432080-T-C
• rs3799419
• NM_003980.6:c.68-10281A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003980.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP7	NM_003980.6	MANE Select	c.68-10281A>G		intron	N/A	NP_003971.1	Q14244-1
	MAP7	NM_001198609.2		c.134-10281A>G		intron	N/A	NP_001185538.1	A0A087WZ40
	MAP7	NM_001388328.1		c.134-10281A>G		intron	N/A	NP_001375257.1	A0A087WZ40

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP7	ENST00000354570.8	TSL:1 MANE Select	c.68-10281A>G		intron	N/A	ENSP00000346581.2	Q14244-1
	MAP7	ENST00000617204.4	TSL:2	c.134-10281A>G		intron	N/A	ENSP00000482335.1	A0A087WZ40
	MAP7	ENST00000877105.1		c.68-10281A>G		intron	N/A	ENSP00000547164.1

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

African (AFR) AF: 0.0786 AC: 3264 AN: 41526

American (AMR) AF: 0.337 AC: 5157 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1181 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1333 AN: 5176

South Asian (SAS) AF: 0.260 AC: 1255 AN: 4822

European-Finnish (FIN) AF: 0.383 AC: 4045 AN: 10558

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25745 AN: 67932

Other (OTH) AF: 0.299 AC: 631 AN: 2108

Alfa AF: 0.335 Hom.: 17499

Bravo AF: 0.272

Asia WGS AF: 0.244 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.74
PhyloP100		-0.31
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: rs3799419; hg19: chr6-136753218; COSMIC: COSV63418422;