Variant 5-61332354-AGCGGCG-AGCGGCGGCG details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_020928.2(ZSWIM6):c.98_100dup(p.Gly33dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,004,548 control chromosomes in the GnomAD database, including 7,053 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1078 hom., cov: 29)

Exomes 𝑓: 0.12 ( 5975 hom. )

Consequence

ZSWIM6
NM_020928.2 inframe_insertion

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.00

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 5-61332354-A-AGCG is Benign according to our data. Variant chr5-61332354-A-AGCG is described in ClinVar as [Likely_benign]. Clinvar id is 437395.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSWIM6	NM_020928.2 linkuse as main transcript	c.98_100dup	p.Gly33dup	inframe_insertion	1/14	ENST00000252744.6	NP_065979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSWIM6	ENST00000252744.6 linkuse as main transcript	c.98_100dup	p.Gly33dup	inframe_insertion	1/14	5	NM_020928.2	ENSP00000252744	P1

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

15129

AN:

138814

Hom.:

1077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0281

Gnomad AMI

AF:

0.0778

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.0819

Gnomad EAS

AF:

0.00210

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.176

Gnomad MID

AF:

0.0714

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.102

GnomAD3 exomes

AF:

0.0695

AC:

AN:

302

Hom.:

AF XY:

0.0795

AC XY:

AN XY:

176

show subpopulations

Gnomad AMR exome

AF:

0.00

Gnomad FIN exome

AF:

0.0500

Gnomad NFE exome

AF:

0.0742

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.121

AC:

104517

AN:

865634

Hom.:

5975

Cov.:

AF XY:

0.120

AC XY:

48763

AN XY:

405888

show subpopulations

Gnomad4 AFR exome

AF:

0.0123

Gnomad4 AMR exome

AF:

0.0871

Gnomad4 ASJ exome

AF:

0.0619

Gnomad4 EAS exome

AF:

0.00140

Gnomad4 SAS exome

AF:

0.127

Gnomad4 FIN exome

AF:

0.0296

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.0952

GnomAD4 genome

AF:

0.109

AC:

15138

AN:

138914

Hom.:

1078

Cov.:

AF XY:

0.113

AC XY:

7626

AN XY:

67772

show subpopulations

Gnomad4 AFR

AF:

0.0280

Gnomad4 AMR

AF:

0.198

Gnomad4 ASJ

AF:

0.0819

Gnomad4 EAS

AF:

0.00211

Gnomad4 SAS

AF:

0.132

Gnomad4 FIN

AF:

0.176

Gnomad4 NFE

AF:

0.139

Gnomad4 OTH

AF:

0.101

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Jul 30, 2015	- -
Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Sep 04, 2015	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 02, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 24, 2024	- -

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