rs7940871

Positions:

• chr11-45206279-C-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+1501C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,076 control chromosomes in the GnomAD database, including 4,858 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 0.24 (4858 hom., cov: 32)
• Consequence: PRDM11 NM_001384648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDM11	NM_001384648.1	c.554+1501C>T		intron_variant		ENST00000683152.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDM11	ENST00000683152.1	c.554+1501C>T		intron_variant			NM_001384648.1	P1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36908 AN: 151958 Hom.: 4855 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.243 AC: 36945 AN: 152076 Hom.: 4858 Cov.: 32 AF XY: 0.241 AC XY: 17946 AN XY: 74336

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.0464

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.224

Alfa AF: 0.280 Hom.: 12543

Bravo AF: 0.231

Asia WGS AF: 0.165 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.60

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

Publications

LitVar

Other links and lift over

dbSNP: rs7940871; hg19: chr11-45227830;