Variant rs1129093 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_007131.5(ZNF75D):c.1434G>A(p.Thr478=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 1,209,169 control chromosomes in the GnomAD database, including 59,305 homozygotes. There are 140,186 hemizygotes in GnomAD. 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 0.28 ( 4158 hom., 9121 hem., cov: 23)

Exomes 𝑓: 0.37 ( 55147 hom. 131065 hem. )

Consequence

ZNF75D
NM_007131.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.63

Variant links:

Genes affected

ZNF75D (HGNC:13145): (zinc finger protein 75D) This gene encodes a protein that likely functions as a transcription factor. The protein, which belongs to the ZNF75 family, includes an N-terminal SCAN domain, a KRAB box, and five C2H2-type zinc finger motifs. Another functional gene belonging to this family is located on chromosome 16, while pseudogenes have been identified on chromosomes 11 and 12. Alternative splicing results in multiple transcripts variants. [provided by RefSeq, Jun 2010]

ZNF75D links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-5.63 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF75D	NM_007131.5 linkuse as main transcript	c.1434G>A	p.Thr478=	synonymous_variant	7/7	ENST00000370766.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF75D	ENST00000370766.8 linkuse as main transcript	c.1434G>A	p.Thr478=	synonymous_variant	7/7	1	NM_007131.5	P2	P51815-1
ZNF75D	ENST00000469456.1 linkuse as main transcript	n.1206G>A		non_coding_transcript_exon_variant	2/2	1
ZNF75D	ENST00000370764.1 linkuse as main transcript	c.1149G>A	p.Thr383=	synonymous_variant	4/4	2		A2	P51815-2
ZNF75D	ENST00000494295.1 linkuse as main transcript	n.828-31459G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

31181

AN:

111592

Hom.:

4160

Cov.:

AF XY:

0.270

AC XY:

9117

AN XY:

33804

show subpopulations

Gnomad AFR

AF:

0.0613

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.0444

Gnomad SAS

AF:

0.0993

Gnomad FIN

AF:

0.363

Gnomad MID

AF:

0.330

Gnomad NFE

AF:

0.417

Gnomad OTH

AF:

0.276

GnomAD3 exomes

AF:

0.299

AC:

54554

AN:

182279

Hom.:

6415

AF XY:

0.297

AC XY:

19860

AN XY:

66843

show subpopulations

Gnomad AFR exome

AF:

0.0551

Gnomad AMR exome

AF:

0.284

Gnomad ASJ exome

AF:

0.340

Gnomad EAS exome

AF:

0.0420

Gnomad SAS exome

AF:

0.103

Gnomad FIN exome

AF:

0.373

Gnomad NFE exome

AF:

0.413

Gnomad OTH exome

AF:

0.323

GnomAD4 exome

AF:

0.369

AC:

405254

AN:

1097520

Hom.:

55147

Cov.:

AF XY:

0.361

AC XY:

131065

AN XY:

363042

show subpopulations

Gnomad4 AFR exome

AF:

0.0483

Gnomad4 AMR exome

AF:

0.279

Gnomad4 ASJ exome

AF:

0.344

Gnomad4 EAS exome

AF:

0.0414

Gnomad4 SAS exome

AF:

0.113

Gnomad4 FIN exome

AF:

0.376

Gnomad4 NFE exome

AF:

0.414

Gnomad4 OTH exome

AF:

0.330

GnomAD4 genome

AF:

0.279

AC:

31173

AN:

111649

Hom.:

4158

Cov.:

AF XY:

0.269

AC XY:

9121

AN XY:

33871

show subpopulations

Gnomad4 AFR

AF:

0.0611

Gnomad4 AMR

AF:

0.281

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.0445

Gnomad4 SAS

AF:

0.0999

Gnomad4 FIN

AF:

0.363

Gnomad4 NFE

AF:

0.417

Gnomad4 OTH

AF:

0.275

Alfa

AF:

0.380

Hom.:

8023

Bravo

AF:

0.265

EpiCase

AF:

0.416

EpiControl

AF:

0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.7

DANN

Benign

0.37

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