dbSNP rs1052581: RPRM:c.*644G>A (chr2-153477592-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 NM_019845.3(RPRM):c.*644G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 139,158 control chromosomes in the GnomAD database, including 544 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 0.085 ( 544 hom., cov: 25)

Exomes 𝑓: 0.033 ( 0 hom. )

Consequence

RPRM
NM_019845.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.04

Publications

6 publications found

Variant links:

Genes affected

RPRM (HGNC:24201): (reprimo, TP53 dependent G2 arrest mediator homolog) Predicted to be involved in regulation of mitotic cell cycle. Predicted to act upstream of or within regulation of cell cycle. Predicted to be integral component of membrane. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

RPRM links:

GALNT13 (HGNC:23242): (polypeptide N-acetylgalactosaminyltransferase 13) The GALNT13 protein is a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAcT; EC 2.4.1.41) family, which initiate O-linked glycosylation of mucins (see MUC3A, MIM 158371) by the initial transfer of N-acetylgalactosamine (GalNAc) with an alpha-linkage to a serine or threonine residue.[supplied by OMIM, Apr 2004]

GALNT13 links:

ENSG00000227400 (HGNC:):

ENSG00000227400 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_019845.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019845.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RPRM	NM_019845.3	MANE Select	c.*644G>A	3_prime_UTR	Exon 1 of 1	NP_062819.1	Q9NS64
GALNT13	NM_001422881.1		c.-239+68351C>T	intron	N/A	NP_001409810.1	Q8IUC8-1
GALNT13	NM_001422882.1		c.-239+139812C>T	intron	N/A	NP_001409811.1	Q8IUC8-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RPRM	ENST00000325926.4	TSL:6 MANE Select	c.*644G>A	3_prime_UTR	Exon 1 of 1	ENSP00000314946.3	Q9NS64
ENSG00000227400	ENST00000424322.1	TSL:4	n.430-55629G>A	intron	N/A
ENSG00000301085	ENST00000776050.1		n.-233C>T	upstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.0848

AC:

11776

AN:

138936

Hom.:

545

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0825

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.0806

Gnomad ASJ

AF:

0.135

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.0423

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.0802

Gnomad OTH

AF:

0.0972

GnomAD4 exome

AF:

0.0333

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0156

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0536

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0847

AC:

11773

AN:

139068

Hom.:

544

Cov.:

AF XY:

0.0846

AC XY:

5664

AN XY:

66980

show subpopulations

African (AFR)

AF:

0.0825

AC:

3161

AN:

38306

American (AMR)

AF:

0.0804

AC:

1113

AN:

13850

Ashkenazi Jewish (ASJ)

AF:

0.135

AC:

445

AN:

3290

East Asian (EAS)

AF:

0.144

AC:

581

AN:

4032

South Asian (SAS)

AF:

0.156

AC:

594

AN:

3804

European-Finnish (FIN)

AF:

0.0423

AC:

359

AN:

8490

Middle Eastern (MID)

AF:

0.148

AC:

AN:

270

European-Non Finnish (NFE)

AF:

0.0801

AC:

5144

AN:

64200

Other (OTH)

AF:

0.0961

AC:

189

AN:

1966

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

490

980

1471

1961

2451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<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:

0.0781

Hom.:

124

Bravo

AF:

0.0864

Asia WGS

AF:

0.139

AC:

487

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over