Variant rs3745453 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001367834.3(ZSWIM4):c.*357A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 201,132 control chromosomes in the GnomAD database, including 12,256 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 0.35 ( 9901 hom., cov: 31)

Exomes 𝑓: 0.29 ( 2355 hom. )

Consequence

ZSWIM4
NM_001367834.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.612

Variant links:

Genes affected

ZSWIM4 (HGNC:25704): (zinc finger SWIM-type containing 4) Predicted to enable zinc ion binding activity. Predicted to be part of Cul2-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ZSWIM4 links:

MIR23AHG (HGNC:27620): (miR-23a/27a/24-2 cluster host gene)

MIR23AHG 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSWIM4	NM_001367834.3 linkuse as main transcript	c.*357A>G		3_prime_UTR_variant	14/14	ENST00000590508.6	NP_001354763.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
ZSWIM4	ENST00000590508.6 linkuse as main transcript	c.*357A>G	3_prime_UTR_variant	14/14	2	NM_001367834.3	ENSP00000468285	P1
MIR23AHG	ENST00000587762.2 linkuse as main transcript	n.11522T>C	non_coding_transcript_exon_variant	1/1
ZSWIM4	ENST00000254323.6 linkuse as main transcript	c.*357A>G	3_prime_UTR_variant	13/13	2		ENSP00000254323

Frequencies

GnomAD3 genomes

AF:

0.355

AC:

53799

AN:

151586

Hom.:

9895

Cov.:

show subpopulations

Gnomad AFR

AF:

0.466

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.236

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.369

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.302

GnomAD4 exome

AF:

0.291

AC:

14398

AN:

49428

Hom.:

2355

Cov.:

AF XY:

0.292

AC XY:

7335

AN XY:

25114

show subpopulations

Gnomad4 AFR exome

AF:

0.432

Gnomad4 AMR exome

AF:

0.267

Gnomad4 ASJ exome

AF:

0.206

Gnomad4 EAS exome

AF:

0.245

Gnomad4 SAS exome

AF:

0.292

Gnomad4 FIN exome

AF:

0.327

Gnomad4 NFE exome

AF:

0.293

Gnomad4 OTH exome

AF:

0.281

GnomAD4 genome

AF:

0.355

AC:

53828

AN:

151704

Hom.:

9901

Cov.:

AF XY:

0.353

AC XY:

26149

AN XY:

74102

show subpopulations

Gnomad4 AFR

AF:

0.465

Gnomad4 AMR

AF:

0.302

Gnomad4 ASJ

AF:

0.262

Gnomad4 EAS

AF:

0.236

Gnomad4 SAS

AF:

0.321

Gnomad4 FIN

AF:

0.369

Gnomad4 NFE

AF:

0.317

Gnomad4 OTH

AF:

0.297

Alfa

AF:

0.318

Hom.:

10018

Bravo

AF:

0.350

Asia WGS

AF:

0.309

AC:

1074

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.5

DANN

Benign

0.55

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