chr2-153477985-C-G

Variant names:

• chr2-153477985-C-G
• rs1063728
• NM_019845.3:c.*251G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_019845.3(RPRM):​c.*251G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 521,670 control chromosomes in the GnomAD database, including 50,692 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 0.39 (13020 hom., cov: 32)
  • Exomes 𝑓: 0.43 (37672 hom.)
• Consequence: RPRM NM_019845.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 9 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPRM	NM_019845.3	c.*251G>C		3_prime_UTR_variant	Exon 1 of 1	ENST00000325926.4	NP_062819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPRM	ENST00000325926.4	c.*251G>C		3_prime_UTR_variant	Exon 1 of 1	6	NM_019845.3	ENSP00000314946.3

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59757 AN: 151934 Hom.: 13016 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.386

GnomAD4 exome AF: 0.431 AC: 159265 AN: 369616 Hom.: 37672 Cov.: 2 AF XY: 0.430 AC XY: 82611 AN XY: 192250

African (AFR) AF: 0.252 AC: 2649 AN: 10500

American (AMR) AF: 0.335 AC: 4906 AN: 14630

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 5223 AN: 11656

East Asian (EAS) AF: 0.0663 AC: 1796 AN: 27104

South Asian (SAS) AF: 0.357 AC: 11143 AN: 31178

European-Finnish (FIN) AF: 0.463 AC: 11893 AN: 25708

Middle Eastern (MID) AF: 0.483 AC: 806 AN: 1670

European-Non Finnish (NFE) AF: 0.495 AC: 111363 AN: 224816

Other (OTH) AF: 0.424 AC: 9486 AN: 22354

GnomAD4 genome AF: 0.393 AC: 59786 AN: 152054 Hom.: 13020 Cov.: 32 AF XY: 0.387 AC XY: 28799 AN XY: 74334

African (AFR) AF: 0.254 AC: 10534 AN: 41474

American (AMR) AF: 0.354 AC: 5414 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3472

East Asian (EAS) AF: 0.0643 AC: 331 AN: 5146

South Asian (SAS) AF: 0.355 AC: 1711 AN: 4820

European-Finnish (FIN) AF: 0.459 AC: 4868 AN: 10596

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33959 AN: 67946

Other (OTH) AF: 0.382 AC: 804 AN: 2106

Alfa AF: 0.445 Hom.: 1986

Bravo AF: 0.376

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.88
PhyloP100		1.3
Mutation Taster		=93/7	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1063728; hg19: chr2-154334499;