Variant rs3217 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_053042.3(ZNF518B):c.*78G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,276,302 control chromosomes in the GnomAD database, including 83,831 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 0.28 ( 7122 hom., cov: 33)

Exomes 𝑓: 0.36 ( 76709 hom. )

Consequence

ZNF518B
NM_053042.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.06

Variant links:

Genes affected

ZNF518B (HGNC:29365): (zinc finger protein 518B) 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]

ZNF518B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF518B	NM_053042.3 linkuse as main transcript	c.*78G>A		3_prime_UTR_variant	3/3	ENST00000326756.4	NP_444270.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF518B	ENST00000326756.4 linkuse as main transcript	c.*78G>A		3_prime_UTR_variant	3/3	3	NM_053042.3	ENSP00000317614	P1

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42584

AN:

152028

Hom.:

7119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.311

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.386

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.362

AC:

406737

AN:

1124156

Hom.:

76709

Cov.:

AF XY:

0.359

AC XY:

201256

AN XY:

561338

show subpopulations

Gnomad4 AFR exome

AF:

0.0997

Gnomad4 AMR exome

AF:

0.212

Gnomad4 ASJ exome

AF:

0.382

Gnomad4 EAS exome

AF:

0.227

Gnomad4 SAS exome

AF:

0.247

Gnomad4 FIN exome

AF:

0.342

Gnomad4 NFE exome

AF:

0.391

Gnomad4 OTH exome

AF:

0.341

GnomAD4 genome

AF:

0.280

AC:

42587

AN:

152146

Hom.:

7122

Cov.:

AF XY:

0.276

AC XY:

20497

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.108

Gnomad4 AMR

AF:

0.253

Gnomad4 ASJ

AF:

0.365

Gnomad4 EAS

AF:

0.231

Gnomad4 SAS

AF:

0.249

Gnomad4 FIN

AF:

0.318

Gnomad4 NFE

AF:

0.386

Gnomad4 OTH

AF:

0.299

Alfa

AF:

0.359

Hom.:

9903

Bravo

AF:

0.268

Asia WGS

AF:

0.260

AC:

904

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.6

DANN

Benign

0.66

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