1-13798732-T-C

Variant names:

• chr1-13798732-T-C
• rs2744692
• NM_001393986.1:c.5036+15901T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393986.1(PRDM2):​c.5036+15901T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,172 control chromosomes in the GnomAD database, including 48,813 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 0.79 (48813 hom., cov: 32)
• Consequence: PRDM2 NM_001393986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393986.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDM2	NM_001393986.1	MANE Select	c.5036+15901T>C		intron	N/A	NP_001380915.1	Q13029-1
	PRDM2	NM_012231.5		c.5036+15901T>C		intron	N/A	NP_036363.2
	PRDM2	NM_001393987.1		c.4433+15901T>C		intron	N/A	NP_001380916.1	Q13029-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDM2	ENST00000311066.10	TSL:5 MANE Select	c.5036+15901T>C		intron	N/A	ENSP00000312352.6	Q13029-1
	PRDM2	ENST00000235372.11	TSL:1	c.5036+15901T>C		intron	N/A	ENSP00000235372.6	Q13029-1
	PRDM2	ENST00000503842.5	TSL:1	c.20-17695T>C		intron	N/A	ENSP00000425028.1	D6RED5

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120625 AN: 152054 Hom.: 48743 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.794 AC: 120758 AN: 152172 Hom.: 48813 Cov.: 32 AF XY: 0.791 AC XY: 58849 AN XY: 74376

African (AFR) AF: 0.952 AC: 39566 AN: 41558

American (AMR) AF: 0.785 AC: 11999 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2580 AN: 3468

East Asian (EAS) AF: 0.861 AC: 4452 AN: 5170

South Asian (SAS) AF: 0.693 AC: 3341 AN: 4824

European-Finnish (FIN) AF: 0.685 AC: 7230 AN: 10552

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.721 AC: 48987 AN: 67988

Other (OTH) AF: 0.805 AC: 1702 AN: 2114

Alfa AF: 0.768 Hom.: 7926

Bravo AF: 0.812

Asia WGS AF: 0.807 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.74
PhyloP100		0.12
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: rs2744692; hg19: chr1-14125227;