rs10242455

Variant names:

• chr7-99642556-A-G
• rs10242455
• NM_001350984.2:c.805+18376A>G

Variant summary

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

The NM_001350984.2(ZSCAN25):​c.805+18376A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,148 control chromosomes in the GnomAD database, including 11,931 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 0.28 (11931 hom., cov: 32)
• Consequence: ZSCAN25 NM_001350984.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 38 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN25	NM_001350984.2	c.805+18376A>G		intron_variant	Intron 7 of 7		NP_001337913.1
ZSCAN25	NM_001350985.2	c.805+18376A>G		intron_variant	Intron 5 of 5		NP_001337914.1
ZSCAN25	XM_011515909.3	c.805+18376A>G		intron_variant	Intron 7 of 7		XP_011514211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42244 AN: 152030 Hom.: 11887 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.234

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.278 AC: 42343 AN: 152148 Hom.: 11931 Cov.: 32 AF XY: 0.277 AC XY: 20591 AN XY: 74398

African (AFR) AF: 0.717 AC: 29719 AN: 41460

American (AMR) AF: 0.222 AC: 3397 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1511 AN: 5174

South Asian (SAS) AF: 0.304 AC: 1466 AN: 4824

European-Finnish (FIN) AF: 0.0649 AC: 689 AN: 10612

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0690 AC: 4694 AN: 68008

Other (OTH) AF: 0.232 AC: 490 AN: 2110

Alfa AF: 0.149 Hom.: 14459

Bravo AF: 0.307

Asia WGS AF: 0.337 AC: 1171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.72
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10242455; hg19: chr7-99240179;