chr15-84616764-T-C

Position:

• chr15-84616764-T-C

Variant summary

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

The NM_181877.4(ZSCAN2):​c.407-3838T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 841,500 control chromosomes in the GnomAD database, including 301,073 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 0.86 (56716 hom., cov: 32)
  • Exomes 𝑓: 0.84 (244357 hom.)
• Consequence: ZSCAN2 NM_181877.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN2	NM_181877.4	c.407-3838T>C		intron_variant		ENST00000546148.6	NP_870992.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN2	ENST00000546148.6	c.407-3838T>C		intron_variant		2	NM_181877.4	ENSP00000445451.1

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131125 AN: 152090 Hom.: 56673 Cov.: 32

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.915

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.841

GnomAD4 exome AF: 0.841 AC: 579692 AN: 689292 Hom.: 244357 AF XY: 0.841 AC XY: 270490 AN XY: 321706

Gnomad4 AFR exome AF: 0.933

Gnomad4 AMR exome AF: 0.718

Gnomad4 ASJ exome AF: 0.871

Gnomad4 EAS exome AF: 0.930

Gnomad4 SAS exome AF: 0.829

Gnomad4 FIN exome AF: 0.802

Gnomad4 NFE exome AF: 0.839

Gnomad4 OTH exome AF: 0.847

GnomAD4 genome AF: 0.862 AC: 131223 AN: 152208 Hom.: 56716 Cov.: 32 AF XY: 0.859 AC XY: 63939 AN XY: 74412

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.837

Alfa AF: 0.845 Hom.: 70059

Bravo AF: 0.860

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.5
DANN	Benign	0.80

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: rs3817193; hg19: chr15-85159995;