rs6011058

Variant names:

• chr20-63725275-C-T
• rs6011058
• NM_181485.3:c.585-7944C>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.585-7944C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,186 control chromosomes in the GnomAD database, including 41,340 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 0.73 (41340 hom., cov: 35)
• Consequence: ZGPAT NM_181485.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 23 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZGPAT	NM_181485.3	c.585-7944C>T		intron_variant	Intron 2 of 6	ENST00000355969.11	NP_852150.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZGPAT	ENST00000355969.11	c.585-7944C>T		intron_variant	Intron 2 of 6	1	NM_181485.3	ENSP00000348242.6

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111166 AN: 152068 Hom.: 41298 Cov.: 35

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.731 AC: 111269 AN: 152186 Hom.: 41340 Cov.: 35 AF XY: 0.730 AC XY: 54309 AN XY: 74386

African (AFR) AF: 0.833 AC: 34595 AN: 41546

American (AMR) AF: 0.721 AC: 11020 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2534 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1956 AN: 5174

South Asian (SAS) AF: 0.729 AC: 3519 AN: 4824

European-Finnish (FIN) AF: 0.745 AC: 7873 AN: 10570

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47379 AN: 67994

Other (OTH) AF: 0.737 AC: 1557 AN: 2112

Alfa AF: 0.711 Hom.: 25700

Bravo AF: 0.731

Asia WGS AF: 0.572 AC: 1992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.62
PhyloP100		0.10
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: rs6011058; hg19: chr20-62356627;