5-61332327-GGCGGCGGCGGCGGCGGCGGGGGCAGCA-G

Variant names:

• chr5-61332327-GGCGGCGGCGGCGGCGGCGGGGGCAGCA-G
• rs1238074721
• NM_020928.2:c.74_100delGGGGCAGCAGCGGCGGCGGCGGCGGCG

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_020928.2(ZSWIM6):​c.74_100delGGGGCAGCAGCGGCGGCGGCGGCGGCG​(p.Gly25_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 0.000248 in 809,216 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. G25G) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.00092 (0 hom., cov: 30)
  • Exomes 𝑓: 0.00016 (0 hom.)
• Consequence: ZSWIM6 NM_020928.2 disruptive_inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.15

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]

LOC105378994 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 5-61332327-GGCGGCGGCGGCGGCGGCGGGGGCAGCA-G is Benign according to our data. Variant chr5-61332327-GGCGGCGGCGGCGGCGGCGGGGGCAGCA-G is described in ClinVar as [Benign]. Clinvar id is 1645734.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd4 at 89 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSWIM6	NM_020928.2	c.74_100delGGGGCAGCAGCGGCGGCGGCGGCGGCG	p.Gly25_Gly33del	disruptive_inframe_deletion	Exon 1 of 14	ENST00000252744.6	NP_065979.1
LOC105378994	XR_007058781.1	n.-138_-112delTGCTGCCCCCGCCGCCGCCGCCGCCGC		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSWIM6	ENST00000252744.6	c.74_100delGGGGCAGCAGCGGCGGCGGCGGCGGCG	p.Gly25_Gly33del	disruptive_inframe_deletion	Exon 1 of 14	5	NM_020928.2	ENSP00000252744.5

Frequencies

GnomAD3 genomes AF: 0.000918 AC: 89 AN: 96924 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000738

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000388

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000225

Gnomad OTH AF: 0.00157

GnomAD4 exome AF: 0.000157 AC: 112 AN: 712226 Hom.: 0 AF XY: 0.000132 AC XY: 44 AN XY: 334552

Gnomad4 AFR exome AF: 0.00174

Gnomad4 AMR exome AF: 0.000636

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000911

Gnomad4 SAS exome AF: 0.000269

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000113

Gnomad4 OTH exome AF: 0.000234

GnomAD4 genome AF: 0.000918 AC: 89 AN: 96990 Hom.: 0 Cov.: 30 AF XY: 0.00101 AC XY: 48 AN XY: 47526

Gnomad4 AFR AF: 0.00229

Gnomad4 AMR AF: 0.000737

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000387

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000225

Gnomad4 OTH AF: 0.00157

Alfa AF: 0.000422 Hom.: 0

Bravo AF: 0.000616

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 15, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1238074721; hg19: chr5-60628154;