rs7128207

Positions:

• chr11-45208510-G-T

Variant summary

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

The NM_001384648.1(PRDM11):​c.554+3732G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,090 control chromosomes in the GnomAD database, including 18,789 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 0.48 (18789 hom., cov: 32)
• Consequence: PRDM11 NM_001384648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDM11	NM_001384648.1	c.554+3732G>T		intron_variant		ENST00000683152.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDM11	ENST00000683152.1	c.554+3732G>T		intron_variant			NM_001384648.1	P1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73704 AN: 151972 Hom.: 18778 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.485 AC: 73758 AN: 152090 Hom.: 18789 Cov.: 32 AF XY: 0.484 AC XY: 36005 AN XY: 74328

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.493

Alfa AF: 0.555 Hom.: 31097

Bravo AF: 0.480

Asia WGS AF: 0.469 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs7128207; hg19: chr11-45230061; COSMIC: COSV55438167; COSMIC: COSV55438167;