rs714215

Positions:

• chr11-45225318-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PRDM11	NM_001384648.1	c.1369+475A>G		intron_variant		ENST00000683152.1	NP_001371577.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDM11	ENST00000683152.1	c.1369+475A>G		intron_variant			NM_001384648.1	ENSP00000507575	P1
	ENST00000527450.1	n.179-9115T>C		intron_variant, non_coding_transcript_variant		4
PRDM11	ENST00000622142.5	c.1369+475A>G		intron_variant		5		ENSP00000480626	P1
PRDM11	ENST00000528980.1	n.464-677A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.555

Alfa AF: 0.655 Hom.: 8941

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714215; hg19: chr11-45246869;