Variant 11-75605876-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The ENST00000304771.8(MAP6):c.1248G>A(p.Pro416=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00541 in 1,614,140 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0037 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0056 ( 38 hom. )

Consequence

MAP6
ENST00000304771.8 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.737

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 11-75605876-C-T is Benign according to our data. Variant chr11-75605876-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 782216.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 38 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP6	NM_033063.2 linkuse as main transcript	c.1248G>A	p.Pro416=	synonymous_variant	3/4	ENST00000304771.8	NP_149052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP6	ENST00000304771.8 linkuse as main transcript	c.1248G>A	p.Pro416=	synonymous_variant	3/4	1	NM_033063.2	ENSP00000307093	A2	Q96JE9-1
MAP6	ENST00000434603.2 linkuse as main transcript	c.1248G>A	p.Pro416=	synonymous_variant	3/3	1		ENSP00000415108	P2	Q96JE9-2
MAP6	ENST00000526740.3 linkuse as main transcript	c.261G>A	p.Pro87=	synonymous_variant	3/4	5		ENSP00000434278	A2	Q96JE9-3

Frequencies

GnomAD3 genomes

AF:

0.00371

AC:

564

AN:

152136

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00126

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00190

Gnomad ASJ

AF:

0.00864

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00456

Gnomad FIN

AF:

0.00245

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00591

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00471

AC:

1177

AN:

249826

Hom.:

AF XY:

0.00474

AC XY:

641

AN XY:

135174

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.000867

Gnomad ASJ exome

AF:

0.0100

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00532

Gnomad FIN exome

AF:

0.00296

Gnomad NFE exome

AF:

0.00684

Gnomad OTH exome

AF:

0.00522

GnomAD4 exome

AF:

0.00559

AC:

8172

AN:

1461886

Hom.:

Cov.:

AF XY:

0.00557

AC XY:

4054

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.000747

Gnomad4 AMR exome

AF:

0.000984

Gnomad4 ASJ exome

AF:

0.00876

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00532

Gnomad4 FIN exome

AF:

0.00384

Gnomad4 NFE exome

AF:

0.00621

Gnomad4 OTH exome

AF:

0.00482

GnomAD4 genome

AF:

0.00370

AC:

564

AN:

152254

Hom.:

Cov.:

AF XY:

0.00348

AC XY:

259

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00125

Gnomad4 AMR

AF:

0.00190

Gnomad4 ASJ

AF:

0.00864

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00456

Gnomad4 FIN

AF:

0.00245

Gnomad4 NFE

AF:

0.00591

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00552

Hom.:

Bravo

AF:

0.00345

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00403

EpiControl

AF:

0.00504

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2023	MAP6: BP4, BP7, BS2 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.3

DANN

Benign

0.49

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