GeneBe

rs565100893

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_020928.2(ZSWIM6):​c.63_74delCGGCGGCGGCGG​(p.Gly22_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 0.00000103 in 969,396 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: 26)
Exomes 𝑓: 0.0000010 ( 0 hom. )

Consequence

ZSWIM6
NM_020928.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZSWIM6NM_020928.2 linkc.63_74delCGGCGGCGGCGG p.Gly22_Gly25del disruptive_inframe_deletion Exon 1 of 14 ENST00000252744.6 NP_065979.1 Q9HCJ5
LOC105378994XR_007058781.1 linkn.-122_-111delGCCGCCGCCGCC upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZSWIM6ENST00000252744.6 linkc.63_74delCGGCGGCGGCGG p.Gly22_Gly25del disruptive_inframe_deletion Exon 1 of 14 5 NM_020928.2 ENSP00000252744.5 Q9HCJ5

Frequencies

GnomAD3 genomes
Cov.:
26
GnomAD4 exome
AF:
0.00000103
AC:
1
AN:
969396
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
457600
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000118
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
26
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

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.

Other links and lift over

dbSNP: rs565100893; hg19: chr5-60628153; API