rs685448

Variant names:

• chr11-75609060-C-T
• rs685448
• NM_033063.2:c.906-738G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

MAP6-AS1 (HGNC:58170):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033063.2. 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
	MAP6	NM_033063.2	MANE Select	c.906-738G>A		intron	N/A	NP_149052.1	Q96JE9-1
	MAP6	NM_207577.1		c.906-738G>A		intron	N/A	NP_997460.1	Q96JE9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP6	ENST00000304771.8	TSL:1 MANE Select	c.906-738G>A		intron	N/A	ENSP00000307093.3	Q96JE9-1
	MAP6	ENST00000434603.2	TSL:1	c.906-738G>A		intron	N/A	ENSP00000415108.2	Q96JE9-2
	MAP6	ENST00000950404.1		c.906-738G>A		intron	N/A	ENSP00000620463.1

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

African (AFR) AF: 0.0114 AC: 474 AN: 41538

American (AMR) AF: 0.0325 AC: 498 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 341 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0298 AC: 144 AN: 4826

European-Finnish (FIN) AF: 0.116 AC: 1225 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4302 AN: 68004

Other (OTH) AF: 0.0482 AC: 102 AN: 2116

Alfa AF: 0.0595 Hom.: 479

Bravo AF: 0.0397

Asia WGS AF: 0.0130 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.5
DANN	Benign	0.83
PhyloP100		-0.19
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: rs685448; hg19: chr11-75320105;