rs1859690

Variant names:

• chr7-99629549-A-G
• rs1859690
• NM_145115.3:c.1164A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_145115.3(ZSCAN25):​c.1164A>G​(p.Glu388Glu) 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
• Publications: 27 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145115.3. 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
	ZSCAN25	NM_145115.3	MANE Select	c.1164A>G	p.Glu388Glu	synonymous	Exon 8 of 8	NP_660090.2
	ZSCAN25	NM_001350979.2		c.1164A>G	p.Glu388Glu	synonymous	Exon 6 of 6	NP_001337908.1
	ZSCAN25	NM_001350980.2		c.1164A>G	p.Glu388Glu	synonymous	Exon 9 of 9	NP_001337909.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN25	ENST00000394152.7	TSL:5 MANE Select	c.1164A>G	p.Glu388Glu	synonymous	Exon 8 of 8	ENSP00000377708.2
	ZSCAN25	ENST00000334715.7	TSL:1	c.1164A>G	p.Glu388Glu	synonymous	Exon 5 of 5	ENSP00000334800.3
	ZSCAN25	ENST00000262941.7	TSL:1	c.927A>G	p.Glu309Glu	synonymous	Exon 3 of 3	ENSP00000262941.7

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

GnomAD2 exomes AF: 0.167 AC: 42006 AN: 251424 AF XY: 0.159

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 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

African (AFR) AF: 0.607 AC: 20318 AN: 33480

American (AMR) AF: 0.218 AC: 9730 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.0696 AC: 1819 AN: 26134

East Asian (EAS) AF: 0.291 AC: 11544 AN: 39698

South Asian (SAS) AF: 0.270 AC: 23286 AN: 86258

European-Finnish (FIN) AF: 0.0703 AC: 3752 AN: 53408

Middle Eastern (MID) AF: 0.0791 AC: 456 AN: 5768

European-Non Finnish (NFE) AF: 0.0668 AC: 74292 AN: 1112010

Other (OTH) AF: 0.133 AC: 8014 AN: 60396

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

African (AFR) AF: 0.582 AC: 24127 AN: 41464

American (AMR) AF: 0.204 AC: 3127 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1558 AN: 5176

South Asian (SAS) AF: 0.304 AC: 1466 AN: 4828

European-Finnish (FIN) AF: 0.0651 AC: 691 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0683 AC: 4644 AN: 68024

Other (OTH) AF: 0.204 AC: 431 AN: 2112

Alfa AF: 0.126 Hom.: 9448

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.4
DANN	Benign	0.53
PhyloP100		-2.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
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: rs1859690; hg19: chr7-99227172; COSMIC: COSV53552417; COSMIC: COSV53552417;