rs1043419

chr2-20248800-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_015317.5(PUM2):c.*2785T>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 0.115 in 152,704 control chromosomes in the GnomAD database, including 1,320 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 0.12 (1317 hom., cov: 33)
  • Exomes 𝑓: 0.13 (3 hom.)
• Consequence: PUM2 NM_015317.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33

Genes affected

PUM2 (HGNC:14958): (pumilio RNA binding family member 2) This gene encodes a protein that belongs to a family of RNA-binding proteins. The encoded protein functions as a translational repressor during embryonic development and cell differentiation. This protein is also thought to be a positive regulator of cell proliferation in adipose-derived stem cells. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PUM2	NM_015317.5	c.*2785T>C		3_prime_UTR_variant	21/21	ENST00000361078.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PUM2	ENST00000361078.7	c.*2785T>C		3_prime_UTR_variant	21/21	2	NM_015317.5	P3
PUM2	ENST00000338086.9	c.*2785T>C		3_prime_UTR_variant	20/20	1		P3
PUM2	ENST00000704930.1	c.*2785T>C		3_prime_UTR_variant	21/21			A1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17533 AN: 152156 Hom.: 1315 Cov.: 33

Gnomad AFR AF: 0.0301

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0575

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.133 AC: 57 AN: 430 Hom.: 3 Cov.: 0 AF XY: 0.112 AC XY: 29 AN XY: 260

Gnomad4 FIN exome AF: 0.132

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.115 AC: 17527 AN: 152274 Hom.: 1317 Cov.: 33 AF XY: 0.114 AC XY: 8499 AN XY: 74448

Gnomad4 AFR AF: 0.0299

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0572

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.127

Alfa AF: 0.157 Hom.: 2846

Bravo AF: 0.108

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	16
Dann	Benign	0.84

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: rs1043419; hg19: chr2-20448561;