Variant 11-75587752-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000304771.8(MAP6):c.1749T>C(p.Asp583=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 1,613,716 control chromosomes in the GnomAD database, including 88,516 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 8735 hom., cov: 31)

Exomes 𝑓: 0.32 ( 79781 hom. )

Consequence

MAP6
ENST00000304771.8 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.795

Variant links:

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 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 11-75587752-A-G is Benign according to our data. Variant chr11-75587752-A-G is described in ClinVar as [Benign]. Clinvar id is 1289911.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.795 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP6	NM_033063.2 linkuse as main transcript	c.1749T>C	p.Asp583=	synonymous_variant	4/4	ENST00000304771.8	NP_149052.1
LOC105369391	NR_145823.1 linkuse as main transcript	n.86+4471A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP6	ENST00000304771.8 linkuse as main transcript	c.1749T>C	p.Asp583=	synonymous_variant	4/4	1	NM_033063.2	ENSP00000307093	A2	Q96JE9-1
	ENST00000527803.1 linkuse as main transcript	n.86+4471A>G		intron_variant, non_coding_transcript_variant		4
MAP6	ENST00000526740.3 linkuse as main transcript	c.762T>C	p.Asp254=	synonymous_variant	4/4	5		ENSP00000434278	A2	Q96JE9-3

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

50179

AN:

151774

Hom.:

8704

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.411

Gnomad AMR

AF:

0.491

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.246

Gnomad SAS

AF:

0.475

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.332

GnomAD3 exomes

AF:

0.369

AC:

92803

AN:

251464

Hom.:

19358

AF XY:

0.366

AC XY:

49730

AN XY:

135902

show subpopulations

Gnomad AFR exome

AF:

0.293

Gnomad AMR exome

AF:

0.624

Gnomad ASJ exome

AF:

0.346

Gnomad EAS exome

AF:

0.235

Gnomad SAS exome

AF:

0.463

Gnomad FIN exome

AF:

0.346

Gnomad NFE exome

AF:

0.306

Gnomad OTH exome

AF:

0.347

GnomAD4 exome

AF:

0.322

AC:

471125

AN:

1461824

Hom.:

79781

Cov.:

AF XY:

0.325

AC XY:

236517

AN XY:

727220

show subpopulations

Gnomad4 AFR exome

AF:

0.297

Gnomad4 AMR exome

AF:

0.613

Gnomad4 ASJ exome

AF:

0.345

Gnomad4 EAS exome

AF:

0.253

Gnomad4 SAS exome

AF:

0.456

Gnomad4 FIN exome

AF:

0.343

Gnomad4 NFE exome

AF:

0.302

Gnomad4 OTH exome

AF:

0.326

GnomAD4 genome

AF:

0.331

AC:

50252

AN:

151892

Hom.:

8735

Cov.:

AF XY:

0.340

AC XY:

25224

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.297

Gnomad4 AMR

AF:

0.491

Gnomad4 ASJ

AF:

0.350

Gnomad4 EAS

AF:

0.246

Gnomad4 SAS

AF:

0.475

Gnomad4 FIN

AF:

0.359

Gnomad4 NFE

AF:

0.305

Gnomad4 OTH

AF:

0.337

Alfa

AF:

0.314

Hom.:

3446

Bravo

AF:

0.340

Asia WGS

AF:

0.406

AC:

1410

AN:

3478

EpiCase

AF:

0.320

EpiControl

AF:

0.303

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.21

DANN

Benign

0.81

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over