6-28435826-T-C

Position:

• chr6-28435826-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001012455.2(ZSCAN23):​c.408+33A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 1,522,896 control chromosomes in the GnomAD database, including 117,749 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.39 (12237 hom., cov: 32)
  • Exomes 𝑓: 0.39 (105512 hom.)
• Consequence: ZSCAN23 NM_001012455.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.88

Genes affected

ZSCAN23 (HGNC:21193): (zinc finger and SCAN domain containing 23) 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]

ZSCAN23 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN23	NM_001012455.2	c.408+33A>G		intron_variant		ENST00000289788.5	NP_001012458.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN23	ENST00000289788.5	c.408+33A>G		intron_variant		1	NM_001012455.2	ENSP00000289788.4
ZSCAN23	ENST00000481983.5	n.408+33A>G		intron_variant		5		ENSP00000435430.1
ZSCAN23	ENST00000486481.1	n.105-219A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59698 AN: 151950 Hom.: 12217 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.406

GnomAD3 exomes AF: 0.351 AC: 57862 AN: 164706 Hom.: 10443 AF XY: 0.349 AC XY: 30311 AN XY: 86948

Gnomad AFR exome AF: 0.503

Gnomad AMR exome AF: 0.337

Gnomad ASJ exome AF: 0.442

Gnomad EAS exome AF: 0.252

Gnomad SAS exome AF: 0.384

Gnomad FIN exome AF: 0.267

Gnomad NFE exome AF: 0.355

Gnomad OTH exome AF: 0.362

GnomAD4 exome AF: 0.388 AC: 532470 AN: 1370828 Hom.: 105512 Cov.: 33 AF XY: 0.387 AC XY: 260370 AN XY: 673592

Gnomad4 AFR exome AF: 0.508

Gnomad4 AMR exome AF: 0.347

Gnomad4 ASJ exome AF: 0.426

Gnomad4 EAS exome AF: 0.292

Gnomad4 SAS exome AF: 0.381

Gnomad4 FIN exome AF: 0.268

Gnomad4 NFE exome AF: 0.395

Gnomad4 OTH exome AF: 0.393

GnomAD4 genome AF: 0.393 AC: 59768 AN: 152068 Hom.: 12237 Cov.: 32 AF XY: 0.385 AC XY: 28607 AN XY: 74334

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.403

Alfa AF: 0.370 Hom.: 10840

Bravo AF: 0.405

Asia WGS AF: 0.349 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.071
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11752919; hg19: chr6-28403603; COSMIC: COSV57043808;