Variant 8-143483735-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015117.3(ZC3H3):c.1716-8150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,120 control chromosomes in the GnomAD database, including 40,118 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 ( 40118 hom., cov: 34)

Consequence

ZC3H3
NM_015117.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.488

Variant links:

Genes affected

ZC3H3 (HGNC:28972): (zinc finger CCCH-type containing 3) Predicted to enable SMAD binding activity. Involved in regulation of mRNA polyadenylation. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZC3H3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
ZC3H3	NM_015117.3 link	c.1716-8150T>C	intron_variant		ENST00000262577.6	NP_055932.2	Q8IXZ2-1
ZC3H3	XM_011516944.3 link	c.*1068T>C	3_prime_UTR_variant	5/5		XP_011515246.2
ZC3H3	XM_011516943.3 link	c.1716-8150T>C	intron_variant			XP_011515245.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZC3H3	ENST00000262577.6 link	c.1716-8150T>C		intron_variant		1	NM_015117.3	ENSP00000262577.5		Q8IXZ2-1

Frequencies

GnomAD3 genomes

AF:

0.726

AC:

110338

AN:

152002

Hom.:

40095

Cov.:

show subpopulations

Gnomad AFR

AF:

0.697

Gnomad AMI

AF:

0.723

Gnomad AMR

AF:

0.736

Gnomad ASJ

AF:

0.803

Gnomad EAS

AF:

0.748

Gnomad SAS

AF:

0.805

Gnomad FIN

AF:

0.774

Gnomad MID

AF:

0.699

Gnomad NFE

AF:

0.723

Gnomad OTH

AF:

0.732

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

GnomAD4 genome

AF:

0.726

AC:

110412

AN:

152120

Hom.:

40118

Cov.:

AF XY:

0.732

AC XY:

54430

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.697

Gnomad4 AMR

AF:

0.736

Gnomad4 ASJ

AF:

0.803

Gnomad4 EAS

AF:

0.748

Gnomad4 SAS

AF:

0.805

Gnomad4 FIN

AF:

0.774

Gnomad4 NFE

AF:

0.723

Gnomad4 OTH

AF:

0.729

Alfa

AF:

0.726

Hom.:

59607

Bravo

AF:

0.719

Asia WGS

AF:

0.783

AC:

2724

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.4

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over