rs4344326

chr1-13717114-G-Achr1-13717114-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393986.1(PRDM2):c.9+1500G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.956 in 152,266 control chromosomes in the GnomAD database, including 69,720 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 0.96 (69720 hom., cov: 31)
• Consequence: PRDM2 NM_001393986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416

Genes affected

PRDM2 (HGNC:9347): (PR/SET domain 2) This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 gene. Although the functions of this protein have not been fully characterized, it may (1) play a role in transcriptional regulation during neuronal differentiation and pathogenesis of retinoblastoma, (2) act as a transcriptional activator of the heme-oxygenase-1 gene, and (3) be a specific effector of estrogen action. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDM2	NM_001393986.1	c.9+1500G>A		intron_variant		ENST00000311066.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDM2	ENST00000311066.10	c.9+1500G>A		intron_variant		5	NM_001393986.1	P1
PRDM2	ENST00000235372.11	c.9+1500G>A		intron_variant		1		P1
PRDM2	ENST00000376048.9	c.9+1500G>A		intron_variant		2
PRDM2	ENST00000484063.6	c.9+1500G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145545 AN: 152148 Hom.: 69694 Cov.: 31

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.962

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.956 AC: 145624 AN: 152266 Hom.: 69720 Cov.: 31 AF XY: 0.959 AC XY: 71370 AN XY: 74460

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.981

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 0.978

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.963

Alfa AF: 0.972 Hom.: 71041

Bravo AF: 0.954

Asia WGS AF: 0.974 AC: 3389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.0
Dann	Benign	0.61

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: rs4344326; hg19: chr1-14043609;