chr2-153477985-C-G

Position:

• chr2-153477985-C-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
RPRM	NM_019845.3	c.*251G>C		3_prime_UTR_variant	1/1	ENST00000325926.4	NP_062819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPRM	ENST00000325926.4	c.*251G>C		3_prime_UTR_variant	1/1		NM_019845.3	ENSP00000314946	P1
	ENST00000424322.1	n.430-56022G>C		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR exome AF: 0.252

Gnomad4 AMR exome AF: 0.335

Gnomad4 ASJ exome AF: 0.448

Gnomad4 EAS exome AF: 0.0663

Gnomad4 SAS exome AF: 0.357

Gnomad4 FIN exome AF: 0.463

Gnomad4 NFE exome AF: 0.495

Gnomad4 OTH exome AF: 0.424

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

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.0643

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.382

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1063728; hg19: chr2-154334499;