chr6-136476619-G-A

Variant names:

• chr6-136476619-G-A
• rs11154872
• NM_003980.6:c.68-54820C>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.68-54820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,104 control chromosomes in the GnomAD database, including 37,641 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 0.66 (37641 hom., cov: 32)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.850
• 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP7	NM_003980.6	c.68-54820C>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.68-54820C>T		intron_variant	Intron 1 of 17	1	NM_003980.6	ENSP00000346581.2

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100281 AN: 151986 Hom.: 37649 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.659 AC: 100285 AN: 152104 Hom.: 37641 Cov.: 32 AF XY: 0.665 AC XY: 49451 AN XY: 74354

African (AFR) AF: 0.274 AC: 11355 AN: 41450

American (AMR) AF: 0.713 AC: 10907 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2893 AN: 3472

East Asian (EAS) AF: 0.591 AC: 3056 AN: 5174

South Asian (SAS) AF: 0.841 AC: 4058 AN: 4824

European-Finnish (FIN) AF: 0.850 AC: 8991 AN: 10576

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56697 AN: 67994

Other (OTH) AF: 0.684 AC: 1446 AN: 2114

Alfa AF: 0.718 Hom.: 7611

Bravo AF: 0.630

Asia WGS AF: 0.664 AC: 2307 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.9
DANN	Benign	0.81
PhyloP100		0.85
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: rs11154872; hg19: chr6-136797757;