rs45465393

Positions:

• chr7-99735407-G-A
• chr7-99735407-G-C
• chr7-99735407-G-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BP6 BS2

The XR_927402.3(ZSCAN25):​n.1456-1285G>A 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 0.00326 in 152,162 control chromosomes in the GnomAD database, including 2 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 0.0033 (2 hom., cov: 32)
• Consequence: ZSCAN25 XR_927402.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997

Genes affected

ZSCAN25 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 7-99735407-G-A is Benign according to our data. Variant chr7-99735407-G-A is described in Lovd as [Likely_benign].
• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN25	XR_007059988.1	n.1429-1285G>A		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_007059989.1	n.1371-1285G>A		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_007059990.1	n.1244-1285G>A		intron_variant, non_coding_transcript_variant
ZSCAN25	XR_927402.3	n.1456-1285G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00326 AC: 496 AN: 152044 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.000556

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000983

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00431

Gnomad OTH AF: 0.00192

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

GnomAD4 genome AF: 0.00326 AC: 496 AN: 152162 Hom.: 2 Cov.: 32 AF XY: 0.00360 AC XY: 268 AN XY: 74392

Gnomad4 AFR AF: 0.000554

Gnomad4 AMR AF: 0.000982

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.0151

Gnomad4 NFE AF: 0.00431

Gnomad4 OTH AF: 0.00190

Alfa AF: 0.00283 Hom.: 2

Bravo AF: 0.00207

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45465393; hg19: chr7-99333030;