rs45467892

Positions:

• chr7-99735374-T-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The XR_927402.3(ZSCAN25):​n.1456-1318T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0248 in 151,580 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.025 (77 hom., cov: 31)
• Consequence: ZSCAN25 XR_927402.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.46

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=-0.92).
• BP6: Variant 7-99735374-T-A is Benign according to our data. Variant chr7-99735374-T-A is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0248 (3766/151580) while in subpopulation NFE AF= 0.0334 (2257/67594). AF 95% confidence interval is 0.0322. There are 77 homozygotes in gnomad4. There are 1836 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 77 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN25	XR_007059988.1	n.1429-1318T>A		intron_variant
ZSCAN25	XR_007059989.1	n.1371-1318T>A		intron_variant
ZSCAN25	XR_007059990.1	n.1244-1318T>A		intron_variant
ZSCAN25	XR_927402.3	n.1456-1318T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0249 AC: 3766 AN: 151464 Hom.: 76 Cov.: 31

Gnomad AFR AF: 0.00926

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0125

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0279

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

GnomAD4 genome AF: 0.0248 AC: 3766 AN: 151580 Hom.: 77 Cov.: 31 AF XY: 0.0248 AC XY: 1836 AN XY: 74082

Gnomad4 AFR AF: 0.00926

Gnomad4 AMR AF: 0.0268

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.0465

Gnomad4 NFE AF: 0.0334

Gnomad4 OTH AF: 0.0276

Alfa AF: 0.0294 Hom.: 12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45467892; hg19: chr7-99332997;