chr15-43370975-A-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGG

Position:

• chr15-43370975-A-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001372080.1(ZSCAN29):​c.-560_-531dupCCGGGGCCGGGGCCGGGGCCGGGGCCGGGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.017 (62 hom., cov: 0)
  • Exomes 𝑓: 0.0070 (12 hom.)
• Consequence: ZSCAN29 NM_001372080.1 5_prime_UTR
• Clinical Significance: Likely 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:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-43370975-A-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGG is Benign according to our data. Variant chr15-43370975-A-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGG is described in ClinVar as [Likely_benign]. Clinvar id is 1208069.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0166 (2495/150544) while in subpopulation NFE AF= 0.0243 (1633/67328). AF 95% confidence interval is 0.0233. There are 62 homozygotes in gnomad4. There are 1225 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 62 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN29	NM_001372080.1	c.-560_-531dupCCGGGGCCGGGGCCGGGGCCGGGGCCGGGG		5_prime_UTR_variant	1/6	ENST00000684362.1	NP_001359009.1
ZSCAN29	XM_047432187.1	c.-880_-851dupCCGGGGCCGGGGCCGGGGCCGGGGCCGGGG		5_prime_UTR_variant	1/6		XP_047288143.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN29	ENST00000684362.1	c.-560_-531dupCCGGGGCCGGGGCCGGGGCCGGGGCCGGGG		5_prime_UTR_variant	1/6		NM_001372080.1	ENSP00000507363.1
TUBGCP4	ENST00000570081.1	n.293+1275_293+1304dupCCCGGCCCCGGCCCCGGCCCCGGCCCCGGC		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0166 AC: 2495 AN: 150428 Hom.: 62 Cov.: 0

Gnomad AFR AF: 0.00418

Gnomad AMI AF: 0.0966

Gnomad AMR AF: 0.0133

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.00868

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0242

Gnomad OTH AF: 0.0102

GnomAD4 exome AF: 0.00698 AC: 760 AN: 108808 Hom.: 12 Cov.: 0 AF XY: 0.00661 AC XY: 388 AN XY: 58710

Gnomad4 AFR exome AF: 0.00154

Gnomad4 AMR exome AF: 0.00131

Gnomad4 ASJ exome AF: 0.00267

Gnomad4 EAS exome AF: 0.00371

Gnomad4 SAS exome AF: 0.00243

Gnomad4 FIN exome AF: 0.0116

Gnomad4 NFE exome AF: 0.00912

Gnomad4 OTH exome AF: 0.00767

GnomAD4 genome AF: 0.0166 AC: 2495 AN: 150544 Hom.: 62 Cov.: 0 AF XY: 0.0167 AC XY: 1225 AN XY: 73436

Gnomad4 AFR AF: 0.00417

Gnomad4 AMR AF: 0.0133

Gnomad4 ASJ AF: 0.00260

Gnomad4 EAS AF: 0.0109

Gnomad4 SAS AF: 0.00869

Gnomad4 FIN AF: 0.0267

Gnomad4 NFE AF: 0.0243

Gnomad4 OTH AF: 0.0101

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 26, 2019

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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;