Variant chr6-65304873-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001271675.2(ZC3H11C):c.2352C>A(p.Gly784Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00041 ( 0 hom., cov: 5)

Exomes 𝑓: 0.00040 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZC3H11C
NM_001271675.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0410

Variant links:

Genes affected

ZC3H11C (HGNC:56304): (zinc finger CCCH-type containing 11C)

ZC3H11C links:

EYS (HGNC:21555): (eyes shut homolog) The product of this gene contains multiple epidermal growth factor (EGF)-like and LamG domains. The protein is expressed in the photoreceptor layer of the retina, and the gene is mutated in autosomal recessive retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

EYS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 6-65304873-C-A is Benign according to our data. Variant chr6-65304873-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2656685.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.041 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZC3H11C	NM_001271675.2 linkuse as main transcript	c.2352C>A	p.Gly784Gly	synonymous_variant	2/2	ENST00000398578.3	NP_001258604.1	P0DQW0A0A8V8TLD8B4DYM8
EYS	NM_001142800.2 linkuse as main transcript	c.1767-8754G>T		intron_variant		ENST00000503581.6	NP_001136272.1	Q5T1H1-1
ZC3H11C	XM_017010889.3 linkuse as main transcript	c.2352C>A	p.Gly784Gly	synonymous_variant	2/2		XP_016866378.1	P0DQW0A0A8V8TLD8
EYS	NM_001292009.2 linkuse as main transcript	c.1767-8754G>T		intron_variant			NP_001278938.1	Q5T1H1-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZC3H11C	ENST00000398578.3 linkuse as main transcript	c.2352C>A	p.Gly784Gly	synonymous_variant	2/2	6	NM_001271675.2	ENSP00000513306.1	P0DQW0A0A8V8TLD8
EYS	ENST00000503581.6 linkuse as main transcript	c.1767-8754G>T		intron_variant		5	NM_001142800.2	ENSP00000424243.1	Q5T1H1-1
EYS	ENST00000370621.7 linkuse as main transcript	c.1767-8754G>T		intron_variant		1		ENSP00000359655.3	Q5T1H1-3

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

29474

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000234

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000408

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000693

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000337

AC:

AN:

32680

Hom.:

AF XY:

0.000531

AC XY:

AN XY:

16948

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000939

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000397

AC:

170

AN:

428338

Hom.:

Cov.:

AF XY:

0.000382

AC XY:

AN XY:

225404

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000502

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000387

Gnomad4 NFE exome

AF:

0.000624

Gnomad4 OTH exome

AF:

0.000322

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000407

AC:

AN:

29474

Hom.:

Cov.:

AF XY:

0.000154

AC XY:

AN XY:

13014

show subpopulations

Gnomad4 AFR

AF:

0.000234

Gnomad4 AMR

AF:

0.000408

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000693

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000297

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

ZC3H11C: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

8.8

DANN

Benign

0.76

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