chr11-75591375-T-C

Variant names:

• chr11-75591375-T-C
• rs666566
• NM_033063.2:c.1317-3191A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033063.2(MAP6):​c.1317-3191A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.047 in 152,314 control chromosomes in the GnomAD database, including 241 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 (241 hom., cov: 33)
• Consequence: MAP6 NM_033063.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• 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]

ENSG00000255326 (HGNC:58170):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP6	NM_033063.2	c.1317-3191A>G		intron_variant	Intron 3 of 3	ENST00000304771.8	NP_149052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP6	ENST00000304771.8	c.1317-3191A>G		intron_variant	Intron 3 of 3	1	NM_033063.2	ENSP00000307093.3

Frequencies

GnomAD3 genomes AF: 0.0471 AC: 7172 AN: 152196 Hom.: 242 Cov.: 33

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0470 AC: 7164 AN: 152314 Hom.: 241 Cov.: 33 AF XY: 0.0488 AC XY: 3635 AN XY: 74480

African (AFR) AF: 0.0115 AC: 480 AN: 41560

American (AMR) AF: 0.0325 AC: 497 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0982 AC: 341 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0296 AC: 143 AN: 4824

European-Finnish (FIN) AF: 0.116 AC: 1235 AN: 10616

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

European-Non Finnish (NFE) AF: 0.0636 AC: 4329 AN: 68030

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

Alfa AF: 0.0397 Hom.: 62

Bravo AF: 0.0399

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	-0.84
CADD	Benign	12
DANN	Benign	0.64
PhyloP100		0.087
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: rs666566; hg19: chr11-75302420;