rs1859690

Positions:

• chr7-99629549-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_145115.3(ZSCAN25):​c.1164A>G​(p.Glu388=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,614,058 control chromosomes in the GnomAD database, including 24,316 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 0.24 (8137 hom., cov: 33)
  • Exomes 𝑓: 0.10 (16179 hom.)
• Consequence: ZSCAN25 NM_145115.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95

Genes affected

ZSCAN25 (HGNC:21961): (zinc finger and SCAN domain containing 25) This gene encodes a protein that bears some similarity to zinc finger proteins, which are involved in DNA binding and protein-protein interactions. Multiple alternatively spliced transcript variants have been identified, but the full-length nature for most of them has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP7: Synonymous conserved (PhyloP=-2.95 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN25	NM_145115.3	c.1164A>G	p.Glu388=	synonymous_variant	8/8	ENST00000394152.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN25	ENST00000394152.7	c.1164A>G	p.Glu388=	synonymous_variant	8/8	5	NM_145115.3	P1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36337 AN: 152070 Hom.: 8120 Cov.: 33

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0683

Gnomad OTH AF: 0.205

GnomAD3 exomes AF: 0.167 AC: 42006 AN: 251424 Hom.: 6353 AF XY: 0.159 AC XY: 21589 AN XY: 135894

Gnomad AFR exome AF: 0.592

Gnomad AMR exome AF: 0.223

Gnomad ASJ exome AF: 0.0688

Gnomad EAS exome AF: 0.297

Gnomad SAS exome AF: 0.280

Gnomad FIN exome AF: 0.0671

Gnomad NFE exome AF: 0.0683

Gnomad OTH exome AF: 0.118

GnomAD4 exome AF: 0.105 AC: 153211 AN: 1461870 Hom.: 16179 Cov.: 32 AF XY: 0.107 AC XY: 77860 AN XY: 727238

Gnomad4 AFR exome AF: 0.607

Gnomad4 AMR exome AF: 0.218

Gnomad4 ASJ exome AF: 0.0696

Gnomad4 EAS exome AF: 0.291

Gnomad4 SAS exome AF: 0.270

Gnomad4 FIN exome AF: 0.0703

Gnomad4 NFE exome AF: 0.0668

Gnomad4 OTH exome AF: 0.133

GnomAD4 genome AF: 0.239 AC: 36403 AN: 152188 Hom.: 8137 Cov.: 33 AF XY: 0.239 AC XY: 17768 AN XY: 74412

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0683

Gnomad4 OTH AF: 0.204

Alfa AF: 0.100 Hom.: 4086

Bravo AF: 0.262

Asia WGS AF: 0.331 AC: 1149 AN: 3478

EpiCase AF: 0.0661

EpiControl AF: 0.0690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.4
DANN	Benign	0.53
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs1859690; hg19: chr7-99227172; COSMIC: COSV53552417; COSMIC: COSV53552417;