rs3811409

Positions:

• chr1-151403108-T-C

Variant summary

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

The ENST00000271715.7(POGZ):​c.*1694A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.056 in 524,316 control chromosomes in the GnomAD database, including 1,283 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 0.064 (615 hom., cov: 33)
  • Exomes 𝑓: 0.053 (668 hom.)
• Consequence: POGZ ENST00000271715.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

Genes affected

POGZ (HGNC:18801): (pogo transposable element derived with ZNF domain) The protein encoded by this gene appears to be a zinc finger protein containing a transposase domain at the C-terminus. This protein was found to interact with the transcription factor SP1 in a yeast two-hybrid system. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POGZ	NM_015100.4	c.*1694A>G		3_prime_UTR_variant	19/19	ENST00000271715.7	NP_055915.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POGZ	ENST00000271715.7	c.*1694A>G		3_prime_UTR_variant	19/19	1	NM_015100.4	ENSP00000271715	P3

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9812 AN: 152168 Hom.: 612 Cov.: 33

Gnomad AFR AF: 0.0411

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0589

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0519

Gnomad OTH AF: 0.0622

GnomAD4 exome AF: 0.0525 AC: 19538 AN: 372030 Hom.: 668 Cov.: 6 AF XY: 0.0515 AC XY: 9050 AN XY: 175674

Gnomad4 AFR exome AF: 0.0346

Gnomad4 AMR exome AF: 0.180

Gnomad4 ASJ exome AF: 0.0142

Gnomad4 EAS exome AF: 0.308

Gnomad4 SAS exome AF: 0.110

Gnomad4 FIN exome AF: 0.0634

Gnomad4 NFE exome AF: 0.0505

Gnomad4 OTH exome AF: 0.0549

GnomAD4 genome AF: 0.0645 AC: 9816 AN: 152286 Hom.: 615 Cov.: 33 AF XY: 0.0669 AC XY: 4980 AN XY: 74466

Gnomad4 AFR AF: 0.0409

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0589

Gnomad4 NFE AF: 0.0519

Gnomad4 OTH AF: 0.0606

Alfa AF: 0.0576 Hom.: 162

Bravo AF: 0.0708

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3811409; hg19: chr1-151375584;