dbSNP rs2209972: MARK2P9:n.605C>T (chr10-92419271-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000430958.1(MARK2P9):n.605C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,038 control chromosomes in the GnomAD database, including 9,476 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 0.33 ( 9473 hom., cov: 32)

Exomes 𝑓: 0.37 ( 3 hom. )

Consequence

MARK2P9
ENST00000430958.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.83

Publications

11 publications found

Variant links:

Genes affected

MARK2P9 (HGNC:39800): (MARK2 pseudogene 9)

MARK2P9 links:

ENSG00000304764 (HGNC:):

ENSG00000304764 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MARK2P9	NR_038243.2 link	n.611C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MARK2P9	ENST00000430958.1 link	n.605C>T		non_coding_transcript_exon_variant	Exon 1 of 2	6
ENSG00000304764	ENST00000806156.1 link	n.1194G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50466

AN:

151890

Hom.:

9476

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.646

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.765

Gnomad SAS

AF:

0.554

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.343

GnomAD4 exome

AF:

0.367

AC:

AN:

Hom.:

Cov.:

AF XY:

0.292

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.318

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.332

AC:

50484

AN:

152008

Hom.:

9473

Cov.:

AF XY:

0.341

AC XY:

25328

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.232

AC:

9630

AN:

41440

American (AMR)

AF:

0.414

AC:

6320

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

1236

AN:

3470

East Asian (EAS)

AF:

0.765

AC:

3943

AN:

5156

South Asian (SAS)

AF:

0.553

AC:

2663

AN:

4812

European-Finnish (FIN)

AF:

0.338

AC:

3574

AN:

10582

Middle Eastern (MID)

AF:

0.357

AC:

105

AN:

294

European-Non Finnish (NFE)

AF:

0.319

AC:

21708

AN:

67972

Other (OTH)

AF:

0.342

AC:

720

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1607

3213

4820

6426

8033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

508

1016

1524

2032

2540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.323

Hom.:

10115

Bravo

AF:

0.336

Asia WGS

AF:

0.586

AC:

2035

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

0.42

(source)

DANN

Benign

0.64

PhyloP100

2.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over