rs10242455

Positions:

• chr7-99642556-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZSCAN25	NM_001350984.2	c.805+18376A>G		intron_variant			NP_001337913.1
ZSCAN25	NM_001350985.2	c.805+18376A>G		intron_variant			NP_001337914.1
ZSCAN25	XM_011515909.3	c.805+18376A>G		intron_variant			XP_011514211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0824

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.0649

Gnomad4 NFE AF: 0.0690

Gnomad4 OTH AF: 0.232

Alfa AF: 0.117 Hom.: 3737

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10242455; hg19: chr7-99240179;