rs528020839

Variant names:

• chr5-61332354-AGCGGCGGCG-A
• rs528020839
• NM_020928.2:c.92_100delGCGGCGGCG

Your query was ambiguous. Multiple possible variants found:

• chr5-61332354-AGCGGCGGCG-A
• chr5-61332354-AGCGGCGGCG-AGCG
• chr5-61332354-AGCGGCGGCG-AGCGGCG
• chr5-61332354-AGCGGCGGCG-AGCGGCGGCGGCG
• chr5-61332354-AGCGGCGGCG-AGCGGCGGCGGCGGCG
• chr5-61332354-AGCGGCGGCG-AGCGGCGGCGGCGGCGGCG

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP3

The ENST00000252744.6(ZSWIM6):​c.92_100delGCGGCGGCG​(p.Gly31_Gly33del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000346 in 866,118 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 29)
  • Exomes 𝑓: 0.0000035 (0 hom.)
• Consequence: ZSWIM6 ENST00000252744.6 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.65
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• acromelic frontonasal dysostosis

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P
• neurodevelopmental disorder with movement abnormalities, abnormal gait, and autistic features

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000288936 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP3: Nonframeshift variant in repetitive region in ENST00000252744.6

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000252744.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSWIM6	NM_020928.2	MANE Select	c.92_100delGCGGCGGCG	p.Gly31_Gly33del	disruptive_inframe_deletion	Exon 1 of 14	NP_065979.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSWIM6	ENST00000252744.6	TSL:5 MANE Select	c.92_100delGCGGCGGCG	p.Gly31_Gly33del	disruptive_inframe_deletion	Exon 1 of 14	ENSP00000252744.5
	ENSG00000288936	ENST00000821437.1		n.-15_-7delCGCCGCCGC		upstream_gene	N/A
	ENSG00000288936	ENST00000821446.1		n.-25_-17delCGCCGCCGC		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome AF: 0.00000346 AC: 3 AN: 866118 Hom.: 0 AF XY: 0.00000246 AC XY: 1 AN XY: 406152

African (AFR) AF: 0.00 AC: 0 AN: 17458

American (AMR) AF: 0.00 AC: 0 AN: 2844

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7290

East Asian (EAS) AF: 0.00 AC: 0 AN: 11462

South Asian (SAS) AF: 0.00 AC: 0 AN: 17774

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6838

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2042

European-Non Finnish (NFE) AF: 0.00000390 AC: 3 AN: 769768

Other (OTH) AF: 0.00 AC: 0 AN: 30642

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs528020839; hg19: chr5-60628181;