chr6-136421997-G-A

Variant names:

• chr6-136421997-G-A
• rs2076193
• NM_003980.6:c.68-198C>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.68-198C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,016 control chromosomes in the GnomAD database, including 33,240 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 (33240 hom., cov: 32)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.765 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.68-198C>T		intron	N/A	NP_003971.1	Q14244-1
	MAP7	NM_001198609.2		c.134-198C>T		intron	N/A	NP_001185538.1	A0A087WZ40
	MAP7	NM_001388328.1		c.134-198C>T		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.68-198C>T		intron	N/A	ENSP00000346581.2	Q14244-1
	MAP7	ENST00000617204.4	TSL:2	c.134-198C>T		intron	N/A	ENSP00000482335.1	A0A087WZ40
	MAP7	ENST00000877105.1		c.68-198C>T		intron	N/A	ENSP00000547164.1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99836 AN: 151898 Hom.: 33230 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.657 AC: 99877 AN: 152016 Hom.: 33240 Cov.: 32 AF XY: 0.662 AC XY: 49152 AN XY: 74280

African (AFR) AF: 0.565 AC: 23419 AN: 41418

American (AMR) AF: 0.665 AC: 10171 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2190 AN: 3470

East Asian (EAS) AF: 0.572 AC: 2952 AN: 5164

South Asian (SAS) AF: 0.786 AC: 3794 AN: 4826

European-Finnish (FIN) AF: 0.732 AC: 7722 AN: 10550

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47603 AN: 67984

Other (OTH) AF: 0.636 AC: 1345 AN: 2114

Alfa AF: 0.684 Hom.: 68721

Bravo AF: 0.644

Asia WGS AF: 0.648 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.15
PhyloP100		-0.36
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: rs2076193; hg19: chr6-136743135;