rs3778314

Variant names:

• chr6-136516923-T-C
• rs3778314
• NM_003980.6:c.67+33419A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-136516923-T-C
• chr6-136516923-T-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.67+33419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 150,420 control chromosomes in the GnomAD database, including 2,459 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 0.11 (2459 hom., cov: 31)
• Consequence: MAP7 NM_003980.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP7	NM_003980.6	c.67+33419A>G		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+33419A>G		intron_variant	Intron 1 of 17	1	NM_003980.6	ENSP00000346581.2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17224 AN: 150316 Hom.: 2448 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.00861

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0125

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.115 AC: 17267 AN: 150420 Hom.: 2459 Cov.: 31 AF XY: 0.112 AC XY: 8244 AN XY: 73298

African (AFR) AF: 0.339 AC: 13792 AN: 40706

American (AMR) AF: 0.0964 AC: 1451 AN: 15056

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.120 AC: 609 AN: 5084

South Asian (SAS) AF: 0.0295 AC: 140 AN: 4752

European-Finnish (FIN) AF: 0.00861 AC: 88 AN: 10218

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0125 AC: 847 AN: 67840

Other (OTH) AF: 0.102 AC: 213 AN: 2092

Alfa AF: 0.0306 Hom.: 80

Bravo AF: 0.133

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.37
PhyloP100		-0.35
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: rs3778314; hg19: chr6-136838061;