rs2315008

Variant names:

• chr20-63712604-T-G
• rs2315008
• NM_181485.3:c.584+3440T>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+3440T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 151,964 control chromosomes in the GnomAD database, including 36,802 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 0.69 (36802 hom., cov: 31)
• Consequence: ZGPAT NM_181485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 81 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=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.705 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZGPAT	NM_181485.3	MANE Select	c.584+3440T>G		intron	N/A	NP_852150.2	A0A0S2Z5X3
	ZGPAT	NM_032527.5		c.584+3440T>G		intron	N/A	NP_115916.3
	ZGPAT	NM_001083113.2		c.584+3440T>G		intron	N/A	NP_001076582.1	A0A0S2Z5X3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZGPAT	ENST00000355969.11	TSL:1 MANE Select	c.584+3440T>G		intron	N/A	ENSP00000348242.6	Q8N5A5-2
	ZGPAT	ENST00000448100.6	TSL:1	c.584+3440T>G		intron	N/A	ENSP00000391176.1	Q8N5A5-2
	ZGPAT	ENST00000357119.8	TSL:1	c.584+3440T>G		intron	N/A	ENSP00000349634.4	Q8N5A5-3

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105157 AN: 151846 Hom.: 36785 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.692 AC: 105217 AN: 151964 Hom.: 36802 Cov.: 31 AF XY: 0.692 AC XY: 51412 AN XY: 74268

African (AFR) AF: 0.710 AC: 29440 AN: 41460

American (AMR) AF: 0.709 AC: 10818 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2514 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1955 AN: 5152

South Asian (SAS) AF: 0.725 AC: 3488 AN: 4812

European-Finnish (FIN) AF: 0.741 AC: 7819 AN: 10546

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.690 AC: 46859 AN: 67954

Other (OTH) AF: 0.705 AC: 1484 AN: 2104

Alfa AF: 0.687 Hom.: 155345

Bravo AF: 0.688

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.9
DANN	Benign	0.92
PhyloP100		0.15
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: rs2315008; hg19: chr20-62343956;