Genetic Variant ZSWIM6:p.Gly24_Gly25del (chr5-61332326-GGGCGGC-G) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_020928.2(ZSWIM6):c.69_74delCGGCGG(p.Gly24_Gly25del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.044 in 1,117,382 control chromosomes in the GnomAD database, including 1,570 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.041 ( 222 hom., cov: 26)

Exomes 𝑓: 0.044 ( 1348 hom. )

Consequence

ZSWIM6
NM_020928.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 3.15

Variant links:

Genes affected

ZSWIM6 (HGNC:29316): (zinc finger SWIM-type containing 6) The protein encoded by this gene contains a zinc finger SWI2/SNF2 and MuDR (SWIM) domain. Proteins with SWIM domains have been found in a diverse number of species and are predicted to interact with DNA or proteins. Mutations in this gene result in acromelic frontonasal dysostosis. [provided by RefSeq, Apr 2017]

ZSWIM6 links:

LOC105378994 (HGNC:):

LOC105378994 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 5-61332326-GGGCGGC-G is Benign according to our data. Variant chr5-61332326-GGGCGGC-G is described in ClinVar as [Likely_benign]. Clinvar id is 218778.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-61332326-GGGCGGC-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSWIM6	NM_020928.2 link	c.69_74delCGGCGG	p.Gly24_Gly25del	disruptive_inframe_deletion	Exon 1 of 14	ENST00000252744.6	NP_065979.1	Q9HCJ5
LOC105378994	XR_007058781.1 link	n.-116_-111delGCCGCC		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSWIM6	ENST00000252744.6 link	c.69_74delCGGCGG	p.Gly24_Gly25del	disruptive_inframe_deletion	Exon 1 of 14	5	NM_020928.2	ENSP00000252744.5		Q9HCJ5

Frequencies

GnomAD3 genomes

AF:

0.0410

AC:

6068

AN:

148034

Hom.:

217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0127

Gnomad AMI

AF:

0.0573

Gnomad AMR

AF:

0.0498

Gnomad ASJ

AF:

0.0199

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.0417

Gnomad MID

AF:

0.0449

Gnomad NFE

AF:

0.0407

Gnomad OTH

AF:

0.0330

GnomAD3 exomes

AF:

0.0175

AC:

AN:

456

Hom.:

AF XY:

0.0240

AC XY:

AN XY:

292

show subpopulations

Gnomad ASJ exome

AF:

0.00

Gnomad FIN exome

AF:

0.0183

Gnomad NFE exome

AF:

0.0174

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0445

AC:

43117

AN:

969252

Hom.:

1348

AF XY:

0.0449

AC XY:

20548

AN XY:

457506

show subpopulations

Gnomad4 AFR exome

AF:

0.0110

Gnomad4 AMR exome

AF:

0.0553

Gnomad4 ASJ exome

AF:

0.0206

Gnomad4 EAS exome

AF:

0.0900

Gnomad4 SAS exome

AF:

0.178

Gnomad4 FIN exome

AF:

0.0365

Gnomad4 NFE exome

AF:

0.0411

Gnomad4 OTH exome

AF:

0.0580

GnomAD4 genome

AF:

0.0411

AC:

6091

AN:

148130

Hom.:

222

Cov.:

AF XY:

0.0448

AC XY:

3235

AN XY:

72240

show subpopulations

Gnomad4 AFR

AF:

0.0130

Gnomad4 AMR

AF:

0.0498

Gnomad4 ASJ

AF:

0.0199

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.183

Gnomad4 FIN

AF:

0.0417

Gnomad4 NFE

AF:

0.0407

Gnomad4 OTH

AF:

0.0399

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 19, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 05, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

May 14, 2015

Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

ZSWIM6-related disorder

Benign:1

Oct 31, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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