rs1043419

Variant names:

• chr2-20248800-A-G
• rs1043419
• NM_015317.5:c.*2785T>C

Variant summary

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

The ENST00000361078.7(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 ENST00000361078.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361078.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PUM2	NM_015317.5	MANE Select	c.*2785T>C		3_prime_UTR	Exon 21 of 21	NP_056132.1
	PUM2	NM_001352917.3		c.*2785T>C		3_prime_UTR	Exon 21 of 21	NP_001339846.1
	PUM2	NM_001352918.2		c.*2785T>C		3_prime_UTR	Exon 21 of 21	NP_001339847.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PUM2	ENST00000361078.7	TSL:2 MANE Select	c.*2785T>C		3_prime_UTR	Exon 21 of 21	ENSP00000354370.4
	PUM2	ENST00000338086.9	TSL:1	c.*2785T>C		3_prime_UTR	Exon 20 of 20	ENSP00000338173.5
	PUM2	ENST00000704930.1		c.*2785T>C		3_prime_UTR	Exon 21 of 21	ENSP00000516061.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.132 AC: 56 AN: 424

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.0299 AC: 1245 AN: 41580

American (AMR) AF: 0.116 AC: 1769 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3470

East Asian (EAS) AF: 0.0572 AC: 297 AN: 5190

South Asian (SAS) AF: 0.194 AC: 938 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1348 AN: 10588

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10841 AN: 68014

Other (OTH) AF: 0.127 AC: 269 AN: 2112

Alfa AF: 0.153 Hom.: 3781

Bravo AF: 0.108

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	16
DANN	Benign	0.84
PhyloP100		2.3
Mutation Taster		=100/0	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: rs1043419; hg19: chr2-20448561;