ENST00000540894.5:n.*428C>T

Variant names:

• chr15-84622468-C-T
• rs11635597
• ENST00000540894.5:n.*428C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000540894.5(ZSCAN2):​n.*428C>T variant causes a non coding transcript exon 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 ENST00000540894.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 22 publications found

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]

ZSCAN2-AS1 (HGNC:56673): (ZSCAN2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540894.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN2	NM_181877.4	MANE Select	c.*428C>T		3_prime_UTR	Exon 3 of 3	NP_870992.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN2	ENST00000540894.5	TSL:1	n.*428C>T		non_coding_transcript_exon	Exon 2 of 3	ENSP00000441855.1
	ZSCAN2	ENST00000546148.6	TSL:2 MANE Select	c.*428C>T		3_prime_UTR	Exon 3 of 3	ENSP00000445451.1
	ZSCAN2	ENST00000540894.5	TSL:1	n.*428C>T		3_prime_UTR	Exon 2 of 3	ENSP00000441855.1

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

African (AFR) AF: 0.0485 AC: 592 AN: 12208

American (AMR) AF: 0.192 AC: 3493 AN: 18194

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 3497 AN: 13772

East Asian (EAS) AF: 0.103 AC: 3151 AN: 30584

South Asian (SAS) AF: 0.201 AC: 9089 AN: 45206

European-Finnish (FIN) AF: 0.223 AC: 9873 AN: 44226

Middle Eastern (MID) AF: 0.395 AC: 1156 AN: 2924

European-Non Finnish (NFE) AF: 0.279 AC: 75797 AN: 271446

Other (OTH) AF: 0.232 AC: 6088 AN: 26234

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

African (AFR) AF: 0.0480 AC: 1993 AN: 41542

American (AMR) AF: 0.206 AC: 3152 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3466

East Asian (EAS) AF: 0.125 AC: 648 AN: 5170

South Asian (SAS) AF: 0.183 AC: 881 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2394 AN: 10562

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18858 AN: 67986

Other (OTH) AF: 0.216 AC: 456 AN: 2112

Alfa AF: 0.242 Hom.: 4644

Bravo AF: 0.190

Asia WGS AF: 0.155 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.63
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11635597; hg19: chr15-85165699;