rs10495150

Variant summary

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

The NM_018650.5(MARK1):​c.910-2403A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,964 control chromosomes in the GnomAD database, including 5,686 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 0.16 ( 5686 hom., cov: 31)

Consequence

MARK1
NM_018650.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.713
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MARK1NM_018650.5 linkuse as main transcriptc.910-2403A>C intron_variant ENST00000366917.6 NP_061120.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MARK1ENST00000366917.6 linkuse as main transcriptc.910-2403A>C intron_variant 1 NM_018650.5 ENSP00000355884 P3Q9P0L2-1

Frequencies

GnomAD3 genomes
AF:
0.163
AC:
24696
AN:
151848
Hom.:
5670
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.516
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0774
Gnomad ASJ
AF:
0.0680
Gnomad EAS
AF:
0.00406
Gnomad SAS
AF:
0.0656
Gnomad FIN
AF:
0.00151
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.0201
Gnomad OTH
AF:
0.125
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.163
AC:
24757
AN:
151964
Hom.:
5686
Cov.:
31
AF XY:
0.159
AC XY:
11785
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.516
Gnomad4 AMR
AF:
0.0771
Gnomad4 ASJ
AF:
0.0680
Gnomad4 EAS
AF:
0.00407
Gnomad4 SAS
AF:
0.0650
Gnomad4 FIN
AF:
0.00151
Gnomad4 NFE
AF:
0.0201
Gnomad4 OTH
AF:
0.125
Alfa
AF:
0.0427
Hom.:
1234
Bravo
AF:
0.185
Asia WGS
AF:
0.0850
AC:
296
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
3.3
DANN
Benign
0.55

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.

Other links and lift over

dbSNP: rs10495150; hg19: chr1-220801974; API