rs714215

Variant names:

• chr11-45225318-A-G
• rs714215
• NM_001384648.1:c.1369+475A>G

Variant summary

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

The NM_001384648.1(PRDM11):​c.1369+475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,954 control chromosomes in the GnomAD database, including 25,925 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 0.56 (25925 hom., cov: 31)
• Consequence: PRDM11 NM_001384648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605
• Publications: 3 publications found

Genes affected

PRDM11 (HGNC:13996): (PR/SET domain 11) Predicted to enable chromatin binding activity. Involved in several processes, including negative regulation of cell growth; positive regulation of fibroblast apoptotic process; and regulation of transcription, DNA-templated. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000254664 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDM11	NM_001384648.1	c.1369+475A>G		intron_variant	Intron 7 of 7	ENST00000683152.1	NP_001371577.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDM11	ENST00000683152.1	c.1369+475A>G		intron_variant	Intron 7 of 7		NM_001384648.1	ENSP00000507575.1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85533 AN: 151836 Hom.: 25906 Cov.: 31

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.563 AC: 85588 AN: 151954 Hom.: 25925 Cov.: 31 AF XY: 0.559 AC XY: 41545 AN XY: 74268

African (AFR) AF: 0.380 AC: 15742 AN: 41428

American (AMR) AF: 0.465 AC: 7101 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2260 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1400 AN: 5140

South Asian (SAS) AF: 0.608 AC: 2924 AN: 4812

European-Finnish (FIN) AF: 0.673 AC: 7088 AN: 10538

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47052 AN: 67976

Other (OTH) AF: 0.555 AC: 1172 AN: 2112

Alfa AF: 0.620 Hom.: 16337

Bravo AF: 0.539

Asia WGS AF: 0.491 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs714215; hg19: chr11-45246869;