NM_001350984.2:c.805+16338G>A

Variant names:

• chr7-99640518-G-A
• rs17161780
• NM_001350984.2:c.805+16338G>A

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+16338G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 152,218 control chromosomes in the GnomAD database, including 679 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 0.069 (679 hom., cov: 32)
• Consequence: ZSCAN25 NM_001350984.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 4 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=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN25	NM_001350984.2	c.805+16338G>A		intron_variant	Intron 7 of 7		NP_001337913.1
ZSCAN25	NM_001350985.2	c.805+16338G>A		intron_variant	Intron 5 of 5		NP_001337914.1
ZSCAN25	XM_011515909.3	c.805+16338G>A		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: 0.0687 AC: 10453 AN: 152100 Hom.: 682 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0687 AC: 10461 AN: 152218 Hom.: 679 Cov.: 32 AF XY: 0.0738 AC XY: 5490 AN XY: 74410

African (AFR) AF: 0.111 AC: 4613 AN: 41506

American (AMR) AF: 0.0934 AC: 1428 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1258 AN: 5168

South Asian (SAS) AF: 0.247 AC: 1192 AN: 4826

European-Finnish (FIN) AF: 0.0147 AC: 156 AN: 10612

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0223 AC: 1520 AN: 68022

Other (OTH) AF: 0.0676 AC: 143 AN: 2114

Alfa AF: 0.0371 Hom.: 217

Bravo AF: 0.0727

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	1.2
DANN	Benign	0.92
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs17161780; hg19: chr7-99238141;