chr1-151404532-TA-T

Position:

• chr1-151404532-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015100.4(POGZ):​c.*269del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 660,890 control chromosomes in the GnomAD database, including 7 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0077 (6 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: POGZ NM_015100.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.191

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 -10 ACMG points.

• BP6: Variant 1-151404532-TA-T is Benign according to our data. Variant chr1-151404532-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 1196316.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POGZ	NM_015100.4	c.*269del		3_prime_UTR_variant	19/19	ENST00000271715.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POGZ	ENST00000271715.7	c.*269del		3_prime_UTR_variant	19/19	1	NM_015100.4	P3

Frequencies

GnomAD3 genomes AF: 0.00772 AC: 1094 AN: 141754 Hom.: 6 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00422

Gnomad ASJ AF: 0.000898

Gnomad EAS AF: 0.00141

Gnomad SAS AF: 0.000887

Gnomad FIN AF: 0.00702

Gnomad MID AF: 0.00662

Gnomad NFE AF: 0.00283

Gnomad OTH AF: 0.00982

GnomAD4 exome AF: 0.167 AC: 86513 AN: 519100 Hom.: 1 Cov.: 3 AF XY: 0.167 AC XY: 40727 AN XY: 243964

Gnomad4 AFR exome AF: 0.195

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.184

Gnomad4 EAS exome AF: 0.179

Gnomad4 SAS exome AF: 0.171

Gnomad4 FIN exome AF: 0.169

Gnomad4 NFE exome AF: 0.165

Gnomad4 OTH exome AF: 0.173

GnomAD4 genome AF: 0.00772 AC: 1094 AN: 141790 Hom.: 6 Cov.: 32 AF XY: 0.00793 AC XY: 544 AN XY: 68580

Gnomad4 AFR AF: 0.0196

Gnomad4 AMR AF: 0.00422

Gnomad4 ASJ AF: 0.000898

Gnomad4 EAS AF: 0.00141

Gnomad4 SAS AF: 0.000668

Gnomad4 FIN AF: 0.00702

Gnomad4 NFE AF: 0.00283

Gnomad4 OTH AF: 0.00975

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 12, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs923196184; hg19: chr1-151377008;