Genetic Variant NM_020928.2:c.72_74dupCGG (chr5-61332326-G-GGGC) – 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.72_74dupCGG(p.Gly25dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 1,116,596 control chromosomes in the GnomAD database, including 11,212 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1478 hom., cov: 26)

Exomes 𝑓: 0.16 ( 9734 hom. )

Consequence

ZSWIM6
NM_020928.2 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.671

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-G-GGGC is Benign according to our data. Variant chr5-61332326-G-GGGC is described in ClinVar as [Benign]. Clinvar id is 1257965.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSWIM6	NM_020928.2 link	c.72_74dupCGG	p.Gly25dup	disruptive_inframe_insertion	Exon 1 of 14	ENST00000252744.6	NP_065979.1	Q9HCJ5
LOC105378994	XR_007058781.1 link	n.-113_-111dupGCC		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSWIM6	ENST00000252744.6 link	c.72_74dupCGG	p.Gly25dup	disruptive_inframe_insertion	Exon 1 of 14	5	NM_020928.2	ENSP00000252744.5		Q9HCJ5

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20172

AN:

147992

Hom.:

1476

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.222

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.00452

Gnomad SAS

AF:

0.0827

Gnomad FIN

AF:

0.0959

Gnomad MID

AF:

0.154

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.161

GnomAD3 exomes

AF:

0.0943

AC:

AN:

456

Hom.:

AF XY:

0.0822

AC XY:

AN XY:

292

show subpopulations

Gnomad ASJ exome

AF:

0.00

Gnomad FIN exome

AF:

0.0183

Gnomad NFE exome

AF:

0.165

Gnomad OTH exome

AF:

0.250

GnomAD4 exome

AF:

0.155

AC:

150298

AN:

968508

Hom.:

9734

Cov.:

AF XY:

0.154

AC XY:

70200

AN XY:

457136

show subpopulations

Gnomad4 AFR exome

AF:

0.0962

Gnomad4 AMR exome

AF:

0.0721

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.00298

Gnomad4 SAS exome

AF:

0.0769

Gnomad4 FIN exome

AF:

0.0540

Gnomad4 NFE exome

AF:

0.165

Gnomad4 OTH exome

AF:

0.144

GnomAD4 genome

AF:

0.136

AC:

20173

AN:

148088

Hom.:

1478

Cov.:

AF XY:

0.131

AC XY:

9458

AN XY:

72220

show subpopulations

Gnomad4 AFR

AF:

0.118

Gnomad4 AMR

AF:

0.132

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.00453

Gnomad4 SAS

AF:

0.0822

Gnomad4 FIN

AF:

0.0959

Gnomad4 NFE

AF:

0.164

Gnomad4 OTH

AF:

0.160

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Sep 03, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

ZSWIM6-related disorder

Benign:1

Feb 08, 2023

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