Variant chr12-133011394-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_019591.4(ZNF26):c.1515C>T(p.Thr505Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 1,611,016 control chromosomes in the GnomAD database, including 370,271 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.67 ( 34596 hom., cov: 33)

Exomes 𝑓: 0.68 ( 335675 hom. )

Consequence

ZNF26
NM_019591.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.83

Variant links:

Genes affected

ZNF26 (HGNC:13053): (zinc finger protein 26) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF26 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 12-133011394-C-T is Benign according to our data. Variant chr12-133011394-C-T is described in ClinVar as [Benign]. Clinvar id is 982073.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.84 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF26	NM_019591.4 link	c.1515C>T	p.Thr505Thr	synonymous_variant	4/4	ENST00000328654.10	NP_062537.2	P17031V9HW07

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF26	ENST00000328654.10 link	c.1515C>T	p.Thr505Thr	synonymous_variant	4/4	1	NM_019591.4	ENSP00000333725.5		P17031
ZNF26	ENST00000534834.1 link	n.4120C>T		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.672

AC:

102057

AN:

151928

Hom.:

34587

Cov.:

show subpopulations

Gnomad AFR

AF:

0.598

Gnomad AMI

AF:

0.666

Gnomad AMR

AF:

0.775

Gnomad ASJ

AF:

0.748

Gnomad EAS

AF:

0.864

Gnomad SAS

AF:

0.766

Gnomad FIN

AF:

0.701

Gnomad MID

AF:

0.785

Gnomad NFE

AF:

0.662

Gnomad OTH

AF:

0.717

GnomAD4 exome

AF:

0.675

AC:

985473

AN:

1458972

Hom.:

335675

Cov.:

AF XY:

0.678

AC XY:

491655

AN XY:

725452

show subpopulations

Gnomad4 AFR exome

AF:

0.593

Gnomad4 AMR exome

AF:

0.843

Gnomad4 ASJ exome

AF:

0.748

Gnomad4 EAS exome

AF:

0.852

Gnomad4 SAS exome

AF:

0.759

Gnomad4 FIN exome

AF:

0.693

Gnomad4 NFE exome

AF:

0.655

Gnomad4 OTH exome

AF:

0.689

GnomAD4 genome

AF:

0.672

AC:

102101

AN:

152044

Hom.:

34596

Cov.:

AF XY:

0.678

AC XY:

50347

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.597

Gnomad4 AMR

AF:

0.775

Gnomad4 ASJ

AF:

0.748

Gnomad4 EAS

AF:

0.864

Gnomad4 SAS

AF:

0.766

Gnomad4 FIN

AF:

0.701

Gnomad4 NFE

AF:

0.662

Gnomad4 OTH

AF:

0.719

Alfa

AF:

0.629

Hom.:

6676

Bravo

AF:

0.676

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Pathology and Clinical Laboratory Medicine, King Fahad Medical City

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

0.46

DANN

Benign

0.73

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