rs45446698

Positions:

• chr7-99735325-T-G

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.1456-1367T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0281 in 558,348 control chromosomes in the GnomAD database, including 303 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 0.026 (82 hom., cov: 31)
  • Exomes 𝑓: 0.029 (221 hom.)
• Consequence: ZSCAN25 XR_927402.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

Genes affected

ZSCAN25 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 7-99735325-T-G is Benign according to our data. Variant chr7-99735325-T-G is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0263 (3992/151922) while in subpopulation NFE AF= 0.0355 (2411/67858). AF 95% confidence interval is 0.0343. There are 82 homozygotes in gnomad4. There are 1961 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 82 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN25	XR_007059988.1	n.1429-1367T>G		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_007059989.1	n.1371-1367T>G		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_007059990.1	n.1244-1367T>G		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_927402.3	n.1456-1367T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0263 AC: 3991 AN: 151804 Hom.: 81 Cov.: 31

Gnomad AFR AF: 0.00984

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0282

Gnomad ASJ AF: 0.0289

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0355

Gnomad OTH AF: 0.0307

GnomAD4 exome AF: 0.0288 AC: 11704 AN: 406426 Hom.: 221 AF XY: 0.0283 AC XY: 6167 AN XY: 218018

Gnomad4 AFR exome AF: 0.00980

Gnomad4 AMR exome AF: 0.0228

Gnomad4 ASJ exome AF: 0.0242

Gnomad4 EAS exome AF: 0.000154

Gnomad4 SAS exome AF: 0.0164

Gnomad4 FIN exome AF: 0.0458

Gnomad4 NFE exome AF: 0.0343

Gnomad4 OTH exome AF: 0.0286

GnomAD4 genome AF: 0.0263 AC: 3992 AN: 151922 Hom.: 82 Cov.: 31 AF XY: 0.0264 AC XY: 1961 AN XY: 74262

Gnomad4 AFR AF: 0.00983

Gnomad4 AMR AF: 0.0281

Gnomad4 ASJ AF: 0.0289

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.0472

Gnomad4 NFE AF: 0.0355

Gnomad4 OTH AF: 0.0304

Alfa AF: 0.0341 Hom.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45446698; hg19: chr7-99332948;