chr1-13717114-G-A

Variant names:

• chr1-13717114-G-A
• rs4344326
• NM_001393986.1:c.9+1500G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDM2	NM_001393986.1	MANE Select	c.9+1500G>A		intron	N/A	NP_001380915.1
	PRDM2	NM_012231.5		c.9+1500G>A		intron	N/A	NP_036363.2
	PRDM2	NM_015866.6		c.9+1500G>A		intron	N/A	NP_056950.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDM2	ENST00000311066.10	TSL:5 MANE Select	c.9+1500G>A		intron	N/A	ENSP00000312352.6
	PRDM2	ENST00000235372.11	TSL:1	c.9+1500G>A		intron	N/A	ENSP00000235372.6
	PRDM2	ENST00000376048.9	TSL:2	c.9+1500G>A		intron	N/A	ENSP00000365216.5

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

African (AFR) AF: 0.902 AC: 37456 AN: 41516

American (AMR) AF: 0.981 AC: 15004 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3352 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5161 AN: 5180

South Asian (SAS) AF: 0.988 AC: 4770 AN: 4828

European-Finnish (FIN) AF: 0.978 AC: 10375 AN: 10610

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66293 AN: 68038

Other (OTH) AF: 0.963 AC: 2035 AN: 2114

Alfa AF: 0.969 Hom.: 92115

Bravo AF: 0.954

Asia WGS AF: 0.974 AC: 3389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.42
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: rs4344326; hg19: chr1-14043609;