rs11635597

Positions:

• chr15-84622468-C-T

Variant summary

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

The NM_181877.4(ZSCAN2):​c.*428C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 616,934 control chromosomes in the GnomAD database, including 18,521 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 0.20 (3718 hom., cov: 32)
  • Exomes 𝑓: 0.24 (14803 hom.)
• Consequence: ZSCAN2 NM_181877.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

ZSCAN2 (HGNC:20994): (zinc finger and SCAN domain containing 2) The protein encoded by this gene contains several copies of zinc finger motif, which is commonly found in transcriptional regulatory proteins. Studies in mice show that this gene is expressed during embryonic development, and specifically in the testis in adult mice, suggesting that it may play a role in regulating genes in germ cells. Alternative splicing of this gene results in several transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ENSG00000276278 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN2	NM_181877.4	c.*428C>T		3_prime_UTR_variant	3/3	ENST00000546148.6	NP_870992.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN2	ENST00000546148.6	c.*428C>T		3_prime_UTR_variant	3/3	2	NM_181877.4	ENSP00000445451.1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29820 AN: 152022 Hom.: 3719 Cov.: 32

Gnomad AFR AF: 0.0481

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.243 AC: 112736 AN: 464794 Hom.: 14803 Cov.: 0 AF XY: 0.243 AC XY: 59744 AN XY: 245570

Gnomad4 AFR exome AF: 0.0485

Gnomad4 AMR exome AF: 0.192

Gnomad4 ASJ exome AF: 0.254

Gnomad4 EAS exome AF: 0.103

Gnomad4 SAS exome AF: 0.201

Gnomad4 FIN exome AF: 0.223

Gnomad4 NFE exome AF: 0.279

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.196 AC: 29814 AN: 152140 Hom.: 3718 Cov.: 32 AF XY: 0.193 AC XY: 14338 AN XY: 74356

Gnomad4 AFR AF: 0.0480

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.216

Alfa AF: 0.243 Hom.: 4014

Bravo AF: 0.190

Asia WGS AF: 0.155 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs11635597; hg19: chr15-85165699;