rs2738758

Variant names:

• chr20-63718273-C-G
• rs2738758
• NM_181485.3:c.584+9109C>G

Your query was ambiguous. Multiple possible variants found:

• chr20-63718273-C-G
• chr20-63718273-C-T

Variant summary

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

The NM_032527.5(ZGPAT):​c.584+9109C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,884 control chromosomes in the GnomAD database, including 3,948 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 0.20 (3948 hom., cov: 30)
• Consequence: ZGPAT NM_032527.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 19 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032527.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZGPAT	NM_181485.3	MANE Select	c.584+9109C>G		intron	N/A	NP_852150.2
	ZGPAT	NM_032527.5		c.584+9109C>G		intron	N/A	NP_115916.3
	ZGPAT	NM_001083113.2		c.584+9109C>G		intron	N/A	NP_001076582.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZGPAT	ENST00000355969.11	TSL:1 MANE Select	c.584+9109C>G		intron	N/A	ENSP00000348242.6
	ZGPAT	ENST00000448100.6	TSL:1	c.584+9109C>G		intron	N/A	ENSP00000391176.1
	ZGPAT	ENST00000357119.8	TSL:1	c.584+9109C>G		intron	N/A	ENSP00000349634.4

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30407 AN: 151766 Hom.: 3949 Cov.: 30

Gnomad AFR AF: 0.0817

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.200 AC: 30413 AN: 151884 Hom.: 3948 Cov.: 30 AF XY: 0.203 AC XY: 15028 AN XY: 74210

African (AFR) AF: 0.0817 AC: 3385 AN: 41456

American (AMR) AF: 0.212 AC: 3230 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 800 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3176 AN: 5154

South Asian (SAS) AF: 0.263 AC: 1265 AN: 4810

European-Finnish (FIN) AF: 0.202 AC: 2122 AN: 10504

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

European-Non Finnish (NFE) AF: 0.232 AC: 15735 AN: 67940

Other (OTH) AF: 0.203 AC: 426 AN: 2102

Alfa AF: 0.0942 Hom.: 147

Bravo AF: 0.199

Asia WGS AF: 0.406 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.17
PhyloP100		-2.0
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: rs2738758; hg19: chr20-62349625;