rs16936667

chr8-70063491-A-G

Variant summary

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

The NM_024504.4(PRDM14):c.1183+2744T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,024 control chromosomes in the GnomAD database, including 4,249 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 0.21 (4249 hom., cov: 31)
• Consequence: PRDM14 NM_024504.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

Genes affected

PRDM14 (HGNC:14001): (PR/SET domain 14) This gene encodes a member of the PRDI-BF1 and RIZ homology domain containing (PRDM) family of transcriptional regulators. The encoded protein may possess histone methyltransferase activity and plays a critical role in cell pluripotency by suppressing the expression of differentiation marker genes. Expression of this gene may play a role in breast cancer. [provided by RefSeq, Dec 2011]

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 (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDM14	NM_024504.4	c.1183+2744T>C		intron_variant		ENST00000276594.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDM14	ENST00000276594.3	c.1183+2744T>C		intron_variant		1	NM_024504.4	P1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32133 AN: 151906 Hom.: 4236 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0881

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.212 AC: 32179 AN: 152024 Hom.: 4249 Cov.: 31 AF XY: 0.208 AC XY: 15461 AN XY: 74300

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.0881

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.192

Alfa AF: 0.175 Hom.: 1508

Bravo AF: 0.221

Asia WGS AF: 0.250 AC: 868 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	3.8
Dann	Benign	0.66

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: rs16936667; hg19: chr8-70975726;