Variant 19-12145543-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_145233.4(ZNF625):c.873A>C(p.Arg291=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 1,613,760 control chromosomes in the GnomAD database, including 170,466 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 0.36 ( 12041 hom., cov: 31)

Exomes 𝑓: 0.46 ( 158425 hom. )

Consequence

ZNF625
NM_145233.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.569

Variant links:

Genes affected

ZNF625 (HGNC:30571): (zinc finger protein 625) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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]

ZNF625 links:

ZNF625-ZNF20 (HGNC:):

ZNF625-ZNF20 links:

Genome browser will be placed here

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=0.569 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ZNF625	NM_145233.4 linkuse as main transcript	c.873A>C	p.Arg291=	synonymous_variant	4/4	ENST00000439556.3	NP_660276.2
ZNF625-ZNF20	NR_037802.1 linkuse as main transcript	n.364+1852A>C		intron_variant, non_coding_transcript_variant
ZNF625	NR_037801.2 linkuse as main transcript	n.1045A>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF625	ENST00000439556.3 linkuse as main transcript	c.873A>C	p.Arg291=	synonymous_variant	4/4	2	NM_145233.4	ENSP00000394380	P1	Q96I27-2
ZNF625	ENST00000455799.1 linkuse as main transcript	c.*683A>C		3_prime_UTR_variant	4/4	1		ENSP00000398518
ZNF625	ENST00000414892.5 linkuse as main transcript	c.188+1852A>C		intron_variant		5		ENSP00000405156

Frequencies

GnomAD3 genomes

AF:

0.359

AC:

54447

AN:

151784

Hom.:

12042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0885

Gnomad AMI

AF:

0.342

Gnomad AMR

AF:

0.368

Gnomad ASJ

AF:

0.451

Gnomad EAS

AF:

0.625

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.478

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.460

Gnomad OTH

AF:

0.394

GnomAD3 exomes

AF:

0.446

AC:

112113

AN:

251424

Hom.:

27111

AF XY:

0.464

AC XY:

63087

AN XY:

135890

show subpopulations

Gnomad AFR exome

AF:

0.0802

Gnomad AMR exome

AF:

0.324

Gnomad ASJ exome

AF:

0.451

Gnomad EAS exome

AF:

0.615

Gnomad SAS exome

AF:

0.588

Gnomad FIN exome

AF:

0.471

Gnomad NFE exome

AF:

0.463

Gnomad OTH exome

AF:

0.463

GnomAD4 exome

AF:

0.459

AC:

670572

AN:

1461858

Hom.:

158425

Cov.:

AF XY:

0.465

AC XY:

337845

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.0719

Gnomad4 AMR exome

AF:

0.331

Gnomad4 ASJ exome

AF:

0.458

Gnomad4 EAS exome

AF:

0.608

Gnomad4 SAS exome

AF:

0.586

Gnomad4 FIN exome

AF:

0.467

Gnomad4 NFE exome

AF:

0.460

Gnomad4 OTH exome

AF:

0.456

GnomAD4 genome

AF:

0.358

AC:

54447

AN:

151902

Hom.:

12041

Cov.:

AF XY:

0.365

AC XY:

27116

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.0883

Gnomad4 AMR

AF:

0.368

Gnomad4 ASJ

AF:

0.451

Gnomad4 EAS

AF:

0.624

Gnomad4 SAS

AF:

0.597

Gnomad4 FIN

AF:

0.478

Gnomad4 NFE

AF:

0.460

Gnomad4 OTH

AF:

0.397

Alfa

AF:

0.428

Hom.:

17361

Bravo

AF:

0.334

EpiCase

AF:

0.475

EpiControl

AF:

0.468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.0

DANN

Benign

0.90

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