rs4646457

chr7-99647457-A-Cchr7-99647457-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011515910.3(ZSCAN25):c.806-14A>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 982,922 control chromosomes in the GnomAD database, including 19,555 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 (11433 hom., cov: 32)
  • Exomes 𝑓: 0.098 (8122 hom.)
• Consequence: ZSCAN25 XM_011515910.3 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

ZSCAN25 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN25	NM_001350984.2	c.806-21638A>C		intron_variant
ZSCAN25	NM_001350985.2	c.806-21638A>C		intron_variant
ZSCAN25	XM_011515909.3	c.806-21638A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42118 AN: 152036 Hom.: 11392 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0774

Gnomad OTH AF: 0.233

GnomAD4 exome AF: 0.0975 AC: 81013 AN: 830768 Hom.: 8122 Cov.: 20 AF XY: 0.0968 AC XY: 37132 AN XY: 383760

Gnomad4 AFR exome AF: 0.754

Gnomad4 AMR exome AF: 0.184

Gnomad4 ASJ exome AF: 0.0720

Gnomad4 EAS exome AF: 0.290

Gnomad4 SAS exome AF: 0.270

Gnomad4 FIN exome AF: 0.0652

Gnomad4 NFE exome AF: 0.0777

Gnomad4 OTH exome AF: 0.142

GnomAD4 genome AF: 0.277 AC: 42214 AN: 152154 Hom.: 11433 Cov.: 32 AF XY: 0.276 AC XY: 20547 AN XY: 74394

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.0830

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0773

Gnomad4 OTH AF: 0.232

Alfa AF: 0.109 Hom.: 2868

Bravo AF: 0.305

Asia WGS AF: 0.337 AC: 1172 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	0.23
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4646457; hg19: chr7-99245080;