Variant rs3737296 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018650.5(MARK1):c.1736+31A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 1,548,832 control chromosomes in the GnomAD database, including 470,088 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 0.81 ( 51198 hom., cov: 31)

Exomes 𝑓: 0.77 ( 418890 hom. )

Consequence

MARK1
NM_018650.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.537

Variant links:

Genes affected

MARK1 (HGNC:6896): (microtubule affinity regulating kinase 1) Enables several functions, including ATP binding activity; phospholipid binding activity; and protein kinase activity. Involved in intracellular signal transduction and protein phosphorylation. Located in cytoplasm; dendrite; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

MARK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MARK1	NM_018650.5 link	c.1736+31A>G		intron_variant		ENST00000366917.6	NP_061120.3	Q9P0L2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MARK1	ENST00000366917.6 link	c.1736+31A>G		intron_variant		1	NM_018650.5	ENSP00000355884.5		Q9P0L2-1

Frequencies

GnomAD3 genomes

AF:

0.815

AC:

123853

AN:

152008

Hom.:

51135

Cov.:

show subpopulations

Gnomad AFR

AF:

0.952

Gnomad AMI

AF:

0.882

Gnomad AMR

AF:

0.758

Gnomad ASJ

AF:

0.732

Gnomad EAS

AF:

0.657

Gnomad SAS

AF:

0.793

Gnomad FIN

AF:

0.763

Gnomad MID

AF:

0.710

Gnomad NFE

AF:

0.770

Gnomad OTH

AF:

0.803

GnomAD3 exomes

AF:

0.757

AC:

185368

AN:

244992

Hom.:

70913

AF XY:

0.760

AC XY:

100699

AN XY:

132558

show subpopulations

Gnomad AFR exome

AF:

0.956

Gnomad AMR exome

AF:

0.641

Gnomad ASJ exome

AF:

0.727

Gnomad EAS exome

AF:

0.664

Gnomad SAS exome

AF:

0.803

Gnomad FIN exome

AF:

0.756

Gnomad NFE exome

AF:

0.767

Gnomad OTH exome

AF:

0.765

GnomAD4 exome

AF:

0.773

AC:

1079193

AN:

1396706

Hom.:

418890

Cov.:

AF XY:

0.773

AC XY:

531998

AN XY:

688538

show subpopulations

Gnomad4 AFR exome

AF:

0.960

Gnomad4 AMR exome

AF:

0.652

Gnomad4 ASJ exome

AF:

0.730

Gnomad4 EAS exome

AF:

0.630

Gnomad4 SAS exome

AF:

0.804

Gnomad4 FIN exome

AF:

0.760

Gnomad4 NFE exome

AF:

0.776

Gnomad4 OTH exome

AF:

0.782

GnomAD4 genome

AF:

0.815

AC:

123976

AN:

152126

Hom.:

51198

Cov.:

AF XY:

0.811

AC XY:

60276

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.952

Gnomad4 AMR

AF:

0.758

Gnomad4 ASJ

AF:

0.732

Gnomad4 EAS

AF:

0.658

Gnomad4 SAS

AF:

0.792

Gnomad4 FIN

AF:

0.763

Gnomad4 NFE

AF:

0.770

Gnomad4 OTH

AF:

0.807

Alfa

AF:

0.757

Hom.:

15808

Bravo

AF:

0.814

Asia WGS

AF:

0.756

AC:

2628

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.50

DANN

Benign

0.38

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over