20-63721274-C-T

Variant names:

• chr20-63721274-C-T
• rs1291213
• NM_181485.3:c.585-11945C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181485.3(ZGPAT):​c.585-11945C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,694 control chromosomes in the GnomAD database, including 3,707 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 0.19 (3707 hom., cov: 30)
• Consequence: ZGPAT NM_181485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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.585-11945C>T		intron	N/A	NP_852150.2
	ZGPAT	NM_032527.5		c.585-11945C>T		intron	N/A	NP_115916.3
	ZGPAT	NM_001083113.2		c.585-11945C>T		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.585-11945C>T		intron	N/A	ENSP00000348242.6
	ZGPAT	ENST00000448100.6	TSL:1	c.585-11945C>T		intron	N/A	ENSP00000391176.1
	ZGPAT	ENST00000357119.8	TSL:1	c.585-11945C>T		intron	N/A	ENSP00000349634.4

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28851 AN: 151576 Hom.: 3709 Cov.: 30

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.190 AC: 28852 AN: 151694 Hom.: 3707 Cov.: 30 AF XY: 0.193 AC XY: 14275 AN XY: 74122

African (AFR) AF: 0.0620 AC: 2565 AN: 41342

American (AMR) AF: 0.206 AC: 3135 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 779 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3145 AN: 5120

South Asian (SAS) AF: 0.253 AC: 1214 AN: 4806

European-Finnish (FIN) AF: 0.198 AC: 2086 AN: 10510

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15250 AN: 67922

Other (OTH) AF: 0.192 AC: 404 AN: 2100

Alfa AF: 0.190 Hom.: 401

Bravo AF: 0.188

Asia WGS AF: 0.395 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.75
PhyloP100		0.21
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: rs1291213; hg19: chr20-62352626;