Genetic Variant ZSWIM6:p.Gly24_Gly33del (chr5-61332326-GGGCGGCGGCGGCGGCGGCGGGGGCAGCAGC-G) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_020928.2(ZSWIM6):c.71_100delGCGGGGGCAGCAGCGGCGGCGGCGGCGGCG(p.Gly24_Gly33del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 1,117,480 control chromosomes in the GnomAD database, including 259 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.012 ( 22 hom., cov: 26)

Exomes 𝑓: 0.021 ( 237 hom. )

Consequence

ZSWIM6
NM_020928.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

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

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-GGGCGGCGGCGGCGGCGGCGGGGGCAGCAGC-G is Benign according to our data. Variant chr5-61332326-GGGCGGCGGCGGCGGCGGCGGGGGCAGCAGC-G is described in ClinVar as [Benign]. Clinvar id is 1249694.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0119 (1760/148130) while in subpopulation NFE AF= 0.0196 (1307/66638). AF 95% confidence interval is 0.0187. There are 22 homozygotes in gnomad4. There are 786 alleles in male gnomad4 subpopulation. Median coverage is 26. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1760 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSWIM6	NM_020928.2 link	c.71_100delGCGGGGGCAGCAGCGGCGGCGGCGGCGGCG	p.Gly24_Gly33del	disruptive_inframe_deletion	Exon 1 of 14	ENST00000252744.6	NP_065979.1	Q9HCJ5
LOC105378994	XR_007058781.1 link	n.-140_-111delGCTGCTGCCCCCGCCGCCGCCGCCGCCGCC		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSWIM6	ENST00000252744.6 link	c.71_100delGCGGGGGCAGCAGCGGCGGCGGCGGCGGCG	p.Gly24_Gly33del	disruptive_inframe_deletion	Exon 1 of 14	5	NM_020928.2	ENSP00000252744.5		Q9HCJ5

Frequencies

GnomAD3 genomes

AF:

0.0119

AC:

1762

AN:

148034

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00371

Gnomad AMI

AF:

0.00991

Gnomad AMR

AF:

0.0132

Gnomad ASJ

AF:

0.00762

Gnomad EAS

AF:

0.000393

Gnomad SAS

AF:

0.00125

Gnomad FIN

AF:

0.00343

Gnomad MID

AF:

0.0160

Gnomad NFE

AF:

0.0196

Gnomad OTH

AF:

0.0133

GnomAD3 exomes

AF:

0.0110

AC:

AN:

456

Hom.:

AF XY:

0.0103

AC XY:

AN XY:

292

show subpopulations

Gnomad ASJ exome

AF:

0.00

Gnomad FIN exome

AF:

0.00459

Gnomad NFE exome

AF:

0.0174

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0210

AC:

20360

AN:

969350

Hom.:

237

AF XY:

0.0213

AC XY:

9743

AN XY:

457572

show subpopulations

Gnomad4 AFR exome

AF:

0.00203

Gnomad4 AMR exome

AF:

0.0108

Gnomad4 ASJ exome

AF:

0.00940

Gnomad4 EAS exome

AF:

0.0000514

Gnomad4 SAS exome

AF:

0.00281

Gnomad4 FIN exome

AF:

0.00695

Gnomad4 NFE exome

AF:

0.0230

Gnomad4 OTH exome

AF:

0.0158

GnomAD4 genome

AF:

0.0119

AC:

1760

AN:

148130

Hom.:

Cov.:

AF XY:

0.0109

AC XY:

786

AN XY:

72240

show subpopulations

Gnomad4 AFR

AF:

0.00370

Gnomad4 AMR

AF:

0.0132

Gnomad4 ASJ

AF:

0.00762

Gnomad4 EAS

AF:

0.000394

Gnomad4 SAS

AF:

0.00125

Gnomad4 FIN

AF:

0.00343

Gnomad4 NFE

AF:

0.0196

Gnomad4 OTH

AF:

0.0131

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 26, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

ZSWIM6-related disorder

Benign:1

Nov 02, 2022

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