rs10495150

Variant names:

• chr1-220628632-A-C
• rs10495150
• NM_018650.5:c.910-2403A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018650.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARK1	NM_018650.5	MANE Select	c.910-2403A>C		intron	N/A	NP_061120.3
	MARK1	NM_001286124.2		c.910-2403A>C		intron	N/A	NP_001273053.1	A0A087X0I6
	MARK1	NM_001286126.2		c.910-2403A>C		intron	N/A	NP_001273055.1	B4DIB3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARK1	ENST00000366917.6	TSL:1 MANE Select	c.910-2403A>C		intron	N/A	ENSP00000355884.5	Q9P0L2-1
	MARK1	ENST00000611084.4	TSL:1	c.910-2403A>C		intron	N/A	ENSP00000483424.1	A0A087X0I6
	MARK1	ENST00000402574.5	TSL:1	c.910-2403A>C		intron	N/A	ENSP00000386017.2	B4DIB3

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24696 AN: 151848 Hom.: 5670 Cov.: 31

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

African (AFR) AF: 0.516 AC: 21345 AN: 41372

American (AMR) AF: 0.0771 AC: 1177 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3470

East Asian (EAS) AF: 0.00407 AC: 21 AN: 5158

South Asian (SAS) AF: 0.0650 AC: 313 AN: 4814

European-Finnish (FIN) AF: 0.00151 AC: 16 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0201 AC: 1366 AN: 67978

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.0648 Hom.: 6401

Bravo AF: 0.185

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.55
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10495150; hg19: chr1-220801974;