Genetic Variant MARK2P9:n.925G>T (chr10-92419591-G-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.925G>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 0.546 in 152,142 control chromosomes in the GnomAD database, including 24,182 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 0.55 ( 24168 hom., cov: 31)

Exomes 𝑓: 0.41 ( 14 hom. )

Consequence

MARK2P9
ENST00000430958.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29

Publications

4 publications found

Variant links:

Genes affected

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

MARK2P9 links:

ENSG00000304764 (HGNC:):

ENSG00000304764 links:

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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=-0.66).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MARK2P9	NR_038243.2 link	n.931G>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.925G>T		non_coding_transcript_exon_variant	Exon 1 of 2	6
ENSG00000304764	ENST00000806156.1 link	n.874C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.546

AC:

82872

AN:

151908

Hom.:

24131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.711

Gnomad AMI

AF:

0.700

Gnomad AMR

AF:

0.528

Gnomad ASJ

AF:

0.421

Gnomad EAS

AF:

0.836

Gnomad SAS

AF:

0.721

Gnomad FIN

AF:

0.448

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.506

GnomAD4 exome

AF:

0.414

AC:

AN:

116

Hom.:

Cov.:

AF XY:

0.384

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.600

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.337

AC:

AN:

Other (OTH)

AF:

0.700

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.546

AC:

82970

AN:

152026

Hom.:

24168

Cov.:

AF XY:

0.551

AC XY:

40944

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.711

AC:

29478

AN:

41464

American (AMR)

AF:

0.529

AC:

8077

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.421

AC:

1462

AN:

3472

East Asian (EAS)

AF:

0.836

AC:

4320

AN:

5168

South Asian (SAS)

AF:

0.721

AC:

3465

AN:

4804

European-Finnish (FIN)

AF:

0.448

AC:

4738

AN:

10580

Middle Eastern (MID)

AF:

0.449

AC:

132

AN:

294

European-Non Finnish (NFE)

AF:

0.436

AC:

29598

AN:

67952

Other (OTH)

AF:

0.506

AC:

1066

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1803

3606

5409

7212

9015

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

716

1432

2148

2864

3580

<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:

0.399

Hom.:

2127

Bravo

AF:

0.558

Asia WGS

AF:

0.750

AC:

2608

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.77

(source)

DANN

Benign

0.27

PhyloP100

1.3

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over