Variant 9-125543111-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001006617.3(MAPKAP1):c.906G>A(p.Lys302=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0086 in 1,614,014 control chromosomes in the GnomAD database, including 92 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0067 ( 11 hom., cov: 32)

Exomes 𝑓: 0.0088 ( 81 hom. )

Consequence

MAPKAP1
NM_001006617.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.635

Variant links:

Genes affected

MAPKAP1 (HGNC:18752): (MAPK associated protein 1) This gene encodes a protein that is highly similar to the yeast SIN1 protein, a stress-activated protein kinase. Alternatively spliced transcript variants encoding distinct isoforms have been described. Alternate polyadenylation sites as well as alternate 3' UTRs have been identified for transcripts of this gene. [provided by RefSeq, Jul 2008]

MAPKAP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 9-125543111-C-T is Benign according to our data. Variant chr9-125543111-C-T is described in ClinVar as [Benign]. Clinvar id is 770956.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.635 with no splicing effect.

BS2

High AC in GnomAd4 at 1017 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAPKAP1	NM_001006617.3 linkuse as main transcript	c.906G>A	p.Lys302=	synonymous_variant	7/12	ENST00000265960.8	NP_001006618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPKAP1	ENST00000265960.8 linkuse as main transcript	c.906G>A	p.Lys302=	synonymous_variant	7/12	1	NM_001006617.3	ENSP00000265960	P1	Q9BPZ7-1

Frequencies

GnomAD3 genomes

AF:

0.00668

AC:

1017

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00159

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0155

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00999

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00636

AC:

1600

AN:

251406

Hom.:

AF XY:

0.00631

AC XY:

858

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00272

Gnomad ASJ exome

AF:

0.00238

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0126

Gnomad NFE exome

AF:

0.0102

Gnomad OTH exome

AF:

0.00603

GnomAD4 exome

AF:

0.00880

AC:

12858

AN:

1461680

Hom.:

Cov.:

AF XY:

0.00870

AC XY:

6328

AN XY:

727166

show subpopulations

Gnomad4 AFR exome

AF:

0.00102

Gnomad4 AMR exome

AF:

0.00295

Gnomad4 ASJ exome

AF:

0.00245

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000162

Gnomad4 FIN exome

AF:

0.0126

Gnomad4 NFE exome

AF:

0.0103

Gnomad4 OTH exome

AF:

0.00750

GnomAD4 genome

AF:

0.00668

AC:

1017

AN:

152334

Hom.:

Cov.:

AF XY:

0.00671

AC XY:

500

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00159

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0155

Gnomad4 NFE

AF:

0.0100

Gnomad4 OTH

AF:

0.00427

Alfa

AF:

0.00868

Hom.:

Bravo

AF:

0.00559

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00840

EpiControl

AF:

0.00853

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

4.6

DANN

Benign

0.61

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