NM_003980.6:c.751+196G>T

Variant names:

• chr6-136377559-C-A
• rs2076192
• NM_003980.6:c.751+196G>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.751+196G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,102 control chromosomes in the GnomAD database, including 42,516 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 (42516 hom., cov: 32)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 6 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=-0.48).
• 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 rank	MANE	Protein	UniProt
MAP7	NM_003980.6	c.751+196G>T		intron_variant	Intron 7 of 17	ENST00000354570.8	NP_003971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP7	ENST00000354570.8	c.751+196G>T		intron_variant	Intron 7 of 17	1	NM_003980.6	ENSP00000346581.2

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112092 AN: 151984 Hom.: 42514 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.737 AC: 112121 AN: 152102 Hom.: 42516 Cov.: 32 AF XY: 0.741 AC XY: 55057 AN XY: 74348

African (AFR) AF: 0.559 AC: 23151 AN: 41438

American (AMR) AF: 0.747 AC: 11414 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2883 AN: 3468

East Asian (EAS) AF: 0.572 AC: 2956 AN: 5166

South Asian (SAS) AF: 0.828 AC: 3991 AN: 4822

European-Finnish (FIN) AF: 0.846 AC: 8965 AN: 10592

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56362 AN: 68014

Other (OTH) AF: 0.742 AC: 1567 AN: 2112

Alfa AF: 0.745 Hom.: 9787

Bravo AF: 0.719

Asia WGS AF: 0.671 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	11
DANN	Benign	0.64
PhyloP100		0.0060
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: rs2076192; hg19: chr6-136698697; COSMIC: COSV63423127;