chr20-63717555-A-G

Variant names:

• chr20-63717555-A-G
• rs6062504
• NM_181485.3:c.584+8391A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 55 publications found

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]

ENSG00000273154 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181485.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZGPAT	NM_181485.3	MANE Select	c.584+8391A>G		intron	N/A	NP_852150.2
	ZGPAT	NM_032527.5		c.584+8391A>G		intron	N/A	NP_115916.3
	ZGPAT	NM_001083113.2		c.584+8391A>G		intron	N/A	NP_001076582.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZGPAT	ENST00000355969.11	TSL:1 MANE Select	c.584+8391A>G		intron	N/A	ENSP00000348242.6
	ZGPAT	ENST00000448100.6	TSL:1	c.584+8391A>G		intron	N/A	ENSP00000391176.1
	ZGPAT	ENST00000357119.8	TSL:1	c.584+8391A>G		intron	N/A	ENSP00000349634.4

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

African (AFR) AF: 0.709 AC: 29349 AN: 41366

American (AMR) AF: 0.719 AC: 10814 AN: 15034

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2514 AN: 3436

East Asian (EAS) AF: 0.420 AC: 1951 AN: 4646

South Asian (SAS) AF: 0.746 AC: 3494 AN: 4682

European-Finnish (FIN) AF: 0.755 AC: 7804 AN: 10334

Middle Eastern (MID) AF: 0.752 AC: 218 AN: 290

European-Non Finnish (NFE) AF: 0.696 AC: 46866 AN: 67326

Other (OTH) AF: 0.717 AC: 1479 AN: 2062

Alfa AF: 0.686 Hom.: 59331

Bravo AF: 0.687

Asia WGS AF: 0.560 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.33
PhyloP100		0.061
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: rs6062504; hg19: chr20-62348907;