20-41185409-A-AG

Position:

• chr20-41185409-A-AG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001384317.1(ZHX3):​c.2861-209dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,154 control chromosomes in the GnomAD database, including 1,165 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (1165 hom., cov: 31)
• Consequence: ZHX3 NM_001384317.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.02

Genes affected

ZHX3 (HGNC:15935): (zinc fingers and homeoboxes 3) This gene encodes a member of the zinc fingers and homeoboxes (ZHX) gene family. The encoded protein contains two C2H2-type zinc fingers and five homeodomains and forms a dimer with itself or with zinc fingers and homeoboxes family member 1. In the nucleus, the dimerized protein interacts with the A subunit of the ubiquitous transcription factor nuclear factor-Y and may function as a transcriptional repressor. [provided by RefSeq, Jul 2008]

PLCG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 20-41185409-A-AG is Benign according to our data. Variant chr20-41185409-A-AG is described in ClinVar as [Benign]. Clinvar id is 1285731.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZHX3	NM_001384317.1	c.2861-209dupC		intron_variant		ENST00000683867.1	NP_001371246.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZHX3	ENST00000683867.1	c.2861-209dupC		intron_variant			NM_001384317.1	ENSP00000506788.1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15471 AN: 152036 Hom.: 1163 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.0320

Gnomad SAS AF: 0.0506

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.102 AC: 15483 AN: 152154 Hom.: 1165 Cov.: 31 AF XY: 0.101 AC XY: 7510 AN XY: 74392

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.0323

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.0920

Gnomad4 NFE AF: 0.0580

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0765 Hom.: 79

Bravo AF: 0.104

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs55792704; hg19: chr20-39814049;