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GeneBe

rs45465393

chr7-99735407-G-Achr7-99735407-G-Cchr7-99735407-G-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.997
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-99735407-G-A is Benign according to our data. Variant chr7-99735407-G-A is described in Lovd as [Likely_benign].
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZSCAN25XR_007059988.1 linkuse as main transcriptn.1429-1285G>A intron_variant, non_coding_transcript_variant
ZSCAN25XR_007059989.1 linkuse as main transcriptn.1371-1285G>A intron_variant, non_coding_transcript_variant
ZSCAN25XR_007059990.1 linkuse as main transcriptn.1244-1285G>A intron_variant, non_coding_transcript_variant
ZSCAN25XR_927402.3 linkuse as main transcriptn.1456-1285G>A intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00326
AC:
496
AN:
152044
Hom.:
2
Cov.:
32
show subpopulations
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00326
AC:
496
AN:
152162
Hom.:
2
Cov.:
32
AF XY:
0.00360
AC XY:
268
AN XY:
74392
show subpopulations
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs45465393; hg19: chr7-99333030; API