NM_024504.4:c.1183+1965G>A

Variant names:

• chr8-70064270-C-T
• rs7010162
• NM_024504.4:c.1183+1965G>A

Variant summary

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

The NM_024504.4(PRDM14):​c.1183+1965G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,488 control chromosomes in the GnomAD database, including 22,646 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 0.53 (22646 hom., cov: 29)
• Consequence: PRDM14 NM_024504.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 17 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDM14	NM_024504.4	c.1183+1965G>A		intron_variant	Intron 5 of 7	ENST00000276594.3	NP_078780.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDM14	ENST00000276594.3	c.1183+1965G>A		intron_variant	Intron 5 of 7	1	NM_024504.4	ENSP00000276594.2

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79675 AN: 151370 Hom.: 22621 Cov.: 29

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.527 AC: 79760 AN: 151488 Hom.: 22646 Cov.: 29 AF XY: 0.532 AC XY: 39391 AN XY: 73980

African (AFR) AF: 0.679 AC: 28023 AN: 41260

American (AMR) AF: 0.606 AC: 9226 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1451 AN: 3466

East Asian (EAS) AF: 0.925 AC: 4753 AN: 5136

South Asian (SAS) AF: 0.612 AC: 2917 AN: 4770

European-Finnish (FIN) AF: 0.427 AC: 4458 AN: 10446

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27396 AN: 67884

Other (OTH) AF: 0.497 AC: 1043 AN: 2100

Alfa AF: 0.446 Hom.: 52807

Bravo AF: 0.547

Asia WGS AF: 0.770 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.63
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7010162; hg19: chr8-70976505;