rs13190937

Positions:

• chr6-28443467-G-A
• chr6-28443467-G-T

Variant summary

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

The NM_001012455.2(ZSCAN23):​c.-146C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,174 control chromosomes in the GnomAD database, including 7,919 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 0.31 (7917 hom., cov: 33)
  • Exomes 𝑓: 0.29 (2 hom.)
• Consequence: ZSCAN23 NM_001012455.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN23	NM_001012455.2	c.-146C>T		5_prime_UTR_variant	1/4	ENST00000289788.5	NP_001012458.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN23	ENST00000289788.5	c.-146C>T		5_prime_UTR_variant	1/4	1	NM_001012455.2	ENSP00000289788	P1
ZSCAN23	ENST00000486481.1	n.36C>T		non_coding_transcript_exon_variant	1/3	2
ZSCAN23	ENST00000481983.5	c.-146C>T		5_prime_UTR_variant, NMD_transcript_variant	1/4	5		ENSP00000435430

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47808 AN: 152032 Hom.: 7908 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.337

GnomAD4 exome AF: 0.292 AC: 7 AN: 24 Hom.: 2 Cov.: 0 AF XY: 0.318 AC XY: 7 AN XY: 22

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.314 AC: 47850 AN: 152150 Hom.: 7917 Cov.: 33 AF XY: 0.306 AC XY: 22732 AN XY: 74400

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.332

Alfa AF: 0.305 Hom.: 10364

Bravo AF: 0.328

Asia WGS AF: 0.181 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13190937; hg19: chr6-28411244;