rs3761121

Positions:

• chr20-63711343-T-C

Variant summary

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

The NM_181485.3(ZGPAT):​c.584+2179T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,276 control chromosomes in the GnomAD database, including 1,282 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 0.11 (1282 hom., cov: 32)
• Consequence: ZGPAT NM_181485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZGPAT	NM_181485.3	c.584+2179T>C		intron_variant		ENST00000355969.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZGPAT	ENST00000355969.11	c.584+2179T>C		intron_variant		1	NM_181485.3	P1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16442 AN: 152158 Hom.: 1276 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.108 AC: 16467 AN: 152276 Hom.: 1282 Cov.: 32 AF XY: 0.108 AC XY: 8064 AN XY: 74456

Gnomad4 AFR AF: 0.0344

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0752

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.139

Alfa AF: 0.125 Hom.: 546

Bravo AF: 0.121

Asia WGS AF: 0.180 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.72

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: rs3761121; hg19: chr20-62342695;