Genetic Variant MRPL2P1:n.575C>T (chr12-89753487-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000546688.1(MRPL2P1):n.575C>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 0.0032 in 557,158 control chromosomes in the GnomAD database, including 27 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 0.0093 ( 23 hom., cov: 31)

Exomes 𝑓: 0.00089 ( 4 hom. )

Consequence

MRPL2P1
ENST00000546688.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.44

Publications

2 publications found

Variant links:

Genes affected

MRPL2P1 (HGNC:29698): (mitochondrial ribosomal protein L2 pseudogene 1)

MRPL2P1 links:

ATP2B1-AS1 (HGNC:27883): (ATP2B1 antisense RNA 1)

ATP2B1-AS1 links:

ENSG00000296746 (HGNC:):

ENSG00000296746 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=-0.56).

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00934 (1420/152024) while in subpopulation AFR AF = 0.0327 (1353/41434). AF 95% confidence interval is 0.0312. There are 23 homozygotes in GnomAd4. There are 655 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 23 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546688.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MRPL2P1	ENST00000546688.1	TSL:6	n.575C>T	non_coding_transcript_exon	Exon 1 of 1
ATP2B1-AS1	ENST00000651272.1		n.359+36124C>T	intron	N/A
ENSG00000296746	ENST00000741520.1		n.176-15050G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00930

AC:

1413

AN:

151906

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0326

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000735

Gnomad OTH

AF:

0.00765

GnomAD4 exome

AF:

0.000891

AC:

361

AN:

405134

Hom.:

Cov.:

AF XY:

0.000699

AC XY:

154

AN XY:

220258

show subpopulations

African (AFR)

AF:

0.0270

AC:

279

AN:

10350

American (AMR)

AF:

0.00162

AC:

AN:

24082

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8058

East Asian (EAS)

AF:

0.00

AC:

AN:

14738

South Asian (SAS)

AF:

0.00

AC:

AN:

49454

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32224

Middle Eastern (MID)

AF:

0.00118

AC:

AN:

2534

European-Non Finnish (NFE)

AF:

0.0000122

AC:

AN:

245202

Other (OTH)

AF:

0.00200

AC:

AN:

18492

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

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:

0.00934

AC:

1420

AN:

152024

Hom.:

Cov.:

AF XY:

0.00882

AC XY:

655

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.0327

AC:

1353

AN:

41434

American (AMR)

AF:

0.00301

AC:

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5174

South Asian (SAS)

AF:

0.00

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10554

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0000736

AC:

AN:

67980

Other (OTH)

AF:

0.00757

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

142

213

284

355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00

Hom.:

1526

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.71

PhyloP100

3.4

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over