15-43370975-ACCCCGG-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001372080.1(ZSCAN29):c.-536_-531del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 258,998 control chromosomes in the GnomAD database, including 27,986 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.45 (18533 hom., cov: 0)
  • Exomes 𝑓: 0.41 (9453 hom.)
• Consequence: ZSCAN29 NM_001372080.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.691

Genes affected

ZSCAN29 (HGNC:26673): (zinc finger and SCAN domain containing 29) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TUBGCP4 (HGNC:16691): (tubulin gamma complex component 4) This gene encodes a component of the gamma-tubulin ring complex, which is required for microtubule nucleation. In mammalian cells, the protein localizes to centrosomes in association with gamma-tubulin. Crystal structure analysis revealed a structure composed of five helical bundles arranged around conserved hydrophobic cores. An exposed surface area located in the C-terminal domain is essential and sufficient for direct binding to gamma-tubulin. Mutations in this gene that alter microtubule organization are associated with microcephaly and chorioretinopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-43370975-ACCCCGG-A is Benign according to our data. Variant chr15-43370975-ACCCCGG-A is described in ClinVar as [Benign]. Clinvar id is 1240667.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN29	NM_001372080.1	c.-536_-531del		5_prime_UTR_variant	1/6	ENST00000684362.1
ZSCAN29	XM_047432187.1	c.-856_-851del		5_prime_UTR_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN29	ENST00000684362.1	c.-536_-531del		5_prime_UTR_variant	1/6		NM_001372080.1	P1
TUBGCP4	ENST00000570081.1	n.293+1299_293+1304del		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.445 AC: 66867 AN: 150360 Hom.: 18476 Cov.: 0

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.413

GnomAD4 exome AF: 0.407 AC: 44152 AN: 108522 Hom.: 9453 AF XY: 0.414 AC XY: 24262 AN XY: 58562

Gnomad4 AFR exome AF: 0.828

Gnomad4 AMR exome AF: 0.415

Gnomad4 ASJ exome AF: 0.459

Gnomad4 EAS exome AF: 0.582

Gnomad4 SAS exome AF: 0.506

Gnomad4 FIN exome AF: 0.260

Gnomad4 NFE exome AF: 0.352

Gnomad4 OTH exome AF: 0.402

GnomAD4 genome AF: 0.445 AC: 66974 AN: 150476 Hom.: 18533 Cov.: 0 AF XY: 0.439 AC XY: 32208 AN XY: 73394

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.416

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 08, 2018

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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: rs11279953; hg19: chr15-43663173;