20-63717555-A-G

Position:

• chr20-63717555-A-G

Variant summary

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

The NM_181485.3(ZGPAT):​c.584+8391A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 150,076 control chromosomes in the GnomAD database, including 36,747 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 0.70 (36747 hom., cov: 30)
• Consequence: ZGPAT NM_181485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZGPAT	NM_181485.3	c.584+8391A>G		intron_variant		ENST00000355969.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZGPAT	ENST00000355969.11	c.584+8391A>G		intron_variant		1	NM_181485.3	P1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 105049 AN: 149960 Hom.: 36730 Cov.: 30

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.700 AC: 105109 AN: 150076 Hom.: 36747 Cov.: 30 AF XY: 0.702 AC XY: 51356 AN XY: 73200

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.717

Alfa AF: 0.699 Hom.: 9188

Bravo AF: 0.687

Asia WGS AF: 0.560 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.33

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: rs6062504; hg19: chr20-62348907;