rs1052581

Variant names:

• chr2-153477592-C-T
• rs1052581
• NM_019845.3:c.*644G>A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 6 publications found

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]

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]

ENSG00000227400 (HGNC:):

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPRM	NM_019845.3	c.*644G>A		3_prime_UTR_variant	Exon 1 of 1	ENST00000325926.4	NP_062819.1
GALNT13	NM_001422881.1	c.-239+68351C>T		intron_variant	Intron 1 of 13		NP_001409810.1
GALNT13	NM_001422882.1	c.-239+139812C>T		intron_variant	Intron 7 of 19		NP_001409811.1
GALNT13	NM_001422883.1	c.-613+144265C>T		intron_variant	Intron 5 of 16		NP_001409812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPRM	ENST00000325926.4	c.*644G>A		3_prime_UTR_variant	Exon 1 of 1	6	NM_019845.3	ENSP00000314946.3
ENSG00000227400	ENST00000424322.1	n.430-55629G>A		intron_variant	Intron 1 of 1	4
ENSG00000301085	ENST00000776050.1	n.-233C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0848 AC: 11776 AN: 138936 Hom.: 545 Cov.: 25

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: 3 AN: 90 Hom.: 0 Cov.: 0 AF XY: 0.0156 AC XY: 1 AN XY: 64

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0536 AC: 3 AN: 56

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0847 AC: 11773 AN: 139068 Hom.: 544 Cov.: 25 AF XY: 0.0846 AC XY: 5664 AN XY: 66980

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: 40 AN: 270

European-Non Finnish (NFE) AF: 0.0801 AC: 5144 AN: 64200

Other (OTH) AF: 0.0961 AC: 189 AN: 1966

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	15
DANN	Benign	0.75
PhyloP100		2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1052581; hg19: chr2-154334106;