15-43370975-A-ACCCCGGCCCCGGCCCCGGCCCCGG

Position:

• chr15-43370975-A-ACCCCGGCCCCGGCCCCGGCCCCGG

Variant summary

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

The NM_001372080.1(ZSCAN29):​c.-554_-531dupCCGGGGCCGGGGCCGGGGCCGGGG 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 0.019 (52 hom., cov: 0)
  • Exomes 𝑓: 0.014 (27 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-ACCCCGGCCCCGGCCCCGGCCCCGG is Benign according to our data. Variant chr15-43370975-A-ACCCCGGCCCCGGCCCCGGCCCCGG is described in ClinVar as [Likely_benign]. Clinvar id is 1197063.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0194 (2916/150560) while in subpopulation NFE AF= 0.0275 (1855/67336). AF 95% confidence interval is 0.0265. There are 52 homozygotes in gnomad4. There are 1375 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 52 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN29	NM_001372080.1	c.-554_-531dupCCGGGGCCGGGGCCGGGGCCGGGG		5_prime_UTR_variant	1/6	ENST00000684362.1	NP_001359009.1
ZSCAN29	XM_047432187.1	c.-874_-851dupCCGGGGCCGGGGCCGGGGCCGGGG		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.-554_-531dupCCGGGGCCGGGGCCGGGGCCGGGG		5_prime_UTR_variant	1/6		NM_001372080.1	ENSP00000507363.1
TUBGCP4	ENST00000570081.1	n.293+1281_293+1304dupCCCGGCCCCGGCCCCGGCCCCGGC		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0194 AC: 2918 AN: 150444 Hom.: 53 Cov.: 0

Gnomad AFR AF: 0.00479

Gnomad AMI AF: 0.00112

Gnomad AMR AF: 0.0201

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0167

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0247

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0275

Gnomad OTH AF: 0.0238

GnomAD4 exome AF: 0.0141 AC: 1530 AN: 108810 Hom.: 27 Cov.: 0 AF XY: 0.0138 AC XY: 811 AN XY: 58718

Gnomad4 AFR exome AF: 0.00277

Gnomad4 AMR exome AF: 0.00710

Gnomad4 ASJ exome AF: 0.00534

Gnomad4 EAS exome AF: 0.00949

Gnomad4 SAS exome AF: 0.0121

Gnomad4 FIN exome AF: 0.0132

Gnomad4 NFE exome AF: 0.0166

Gnomad4 OTH exome AF: 0.0139

GnomAD4 genome AF: 0.0194 AC: 2916 AN: 150560 Hom.: 52 Cov.: 0 AF XY: 0.0187 AC XY: 1375 AN XY: 73444

Gnomad4 AFR AF: 0.00478

Gnomad4 AMR AF: 0.0201

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.0167

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.0247

Gnomad4 NFE AF: 0.0275

Gnomad4 OTH AF: 0.0235

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

Jul 31, 2018

- -

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;