Variant chr6-43337359-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_014345.3(ZNF318):c.6639G>A(p.Ser2213=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00161 in 1,614,102 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0016 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0016 ( 20 hom. )

Consequence

ZNF318
NM_014345.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.213

Variant links:

Genes affected

ZNF318 (HGNC:13578): (zinc finger protein 318) Predicted to enable protein heterodimerization activity and protein homodimerization activity. Predicted to be involved in negative regulation of transcription, DNA-templated and positive regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF318 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 6-43337359-C-T is Benign according to our data. Variant chr6-43337359-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 777809.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.213 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0016 (2343/1461824) while in subpopulation MID AF= 0.0284 (164/5768). AF 95% confidence interval is 0.0249. There are 20 homozygotes in gnomad4_exome. There are 1189 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF318	NM_014345.3 linkuse as main transcript	c.6639G>A	p.Ser2213=	synonymous_variant	10/10	ENST00000361428.3	NP_055160.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF318	ENST00000361428.3 linkuse as main transcript	c.6639G>A	p.Ser2213=	synonymous_variant	10/10	1	NM_014345.3	ENSP00000354964	P1	Q5VUA4-1
ZNF318	ENST00000605935.5 linkuse as main transcript	c.3276+5317G>A		intron_variant, NMD_transcript_variant		1		ENSP00000475748		Q5VUA4-2
ZNF318	ENST00000606599.1 linkuse as main transcript	c.161+5317G>A		intron_variant		2		ENSP00000475511

Frequencies

GnomAD3 genomes

AF:

0.00165

AC:

251

AN:

152160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.0277

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00140

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00222

AC:

556

AN:

250824

Hom.:

AF XY:

0.00228

AC XY:

309

AN XY:

135546

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.00142

Gnomad ASJ exome

AF:

0.0293

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000588

Gnomad FIN exome

AF:

0.0000926

Gnomad NFE exome

AF:

0.00134

Gnomad OTH exome

AF:

0.00606

GnomAD4 exome

AF:

0.00160

AC:

2343

AN:

1461824

Hom.:

Cov.:

AF XY:

0.00163

AC XY:

1189

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.000568

Gnomad4 AMR exome

AF:

0.00168

Gnomad4 ASJ exome

AF:

0.0286

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000499

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000969

Gnomad4 OTH exome

AF:

0.00359

GnomAD4 genome

AF:

0.00165

AC:

251

AN:

152278

Hom.:

Cov.:

AF XY:

0.00158

AC XY:

118

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.000217

Gnomad4 AMR

AF:

0.00177

Gnomad4 ASJ

AF:

0.0277

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.00140

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00500

Hom.:

Bravo

AF:

0.00174

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2022	ZNF318: BP4, BP7 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.0

DANN

Benign

0.29

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over