rs6062509

chr20-63731211-G-T

Variant summary

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

The NM_181485.3(ZGPAT):c.585-2008G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,094 control chromosomes in the GnomAD database, including 43,975 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 0.75 (43975 hom., cov: 31)
• Consequence: ZGPAT NM_181485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

ZGPAT (HGNC:15948): (zinc finger CCCH-type and G-patch domain containing) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of epidermal growth factor-activated receptor activity and negative regulation of transcription by RNA polymerase II. Located in nucleoplasm and plasma membrane. [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=-1.12).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZGPAT	NM_181485.3	c.585-2008G>T		intron_variant		ENST00000355969.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZGPAT	ENST00000355969.11	c.585-2008G>T		intron_variant		1	NM_181485.3	P1

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114145 AN: 151976 Hom.: 43925 Cov.: 31

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.751 AC: 114258 AN: 152094 Hom.: 43975 Cov.: 31 AF XY: 0.749 AC XY: 55679 AN XY: 74322

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.753

Alfa AF: 0.726 Hom.: 10495

Bravo AF: 0.754

Asia WGS AF: 0.576 AC: 2004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	1.0
Dann	Benign	0.77

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: rs6062509; hg19: chr20-62362563;