11-75609060-C-T

Position:

• chr11-75609060-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033063.2(MAP6):​c.906-738G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 152,232 control chromosomes in the GnomAD database, including 237 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 0.047 (237 hom., cov: 33)
• Consequence: MAP6 NM_033063.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

Genes affected

MAP6 (HGNC:6868): (microtubule associated protein 6) This gene encodes a microtubule-associated protein. The encoded protein is a calmodulin-binding and calmodulin-regulated protein that is involved in microtubule stabilization. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP6	NM_033063.2	c.906-738G>A		intron_variant		ENST00000304771.8	NP_149052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP6	ENST00000304771.8	c.906-738G>A		intron_variant		1	NM_033063.2	ENSP00000307093	A2
MAP6	ENST00000434603.2	c.906-738G>A		intron_variant		1		ENSP00000415108	P2
MAP6	ENST00000526740.3	c.-82-738G>A		intron_variant		5		ENSP00000434278	A2

Frequencies

GnomAD3 genomes AF: 0.0469 AC: 7131 AN: 152114 Hom.: 238 Cov.: 33

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0468 AC: 7123 AN: 152232 Hom.: 237 Cov.: 33 AF XY: 0.0485 AC XY: 3607 AN XY: 74422

Gnomad4 AFR AF: 0.0114

Gnomad4 AMR AF: 0.0325

Gnomad4 ASJ AF: 0.0983

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0633

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0610 Hom.: 396

Bravo AF: 0.0397

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.5
DANN	Benign	0.83

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

Publications

LitVar

Other links and lift over

dbSNP: rs685448; hg19: chr11-75320105;