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GeneBe

rs45494802

chr7-99735377-A-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The XR_927402.3(ZSCAN25):n.1456-1315A>T 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 0.0247 in 151,524 control chromosomes in the GnomAD database, including 74 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 ( 74 hom., cov: 31)

Consequence

ZSCAN25
XR_927402.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.102
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 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=-0.92).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-99735377-A-T is Benign according to our data. Variant chr7-99735377-A-T is described in Lovd as [Likely_benign].
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0247 (3740/151524) while in subpopulation NFE AF= 0.0332 (2246/67572). AF 95% confidence interval is 0.0321. There are 74 homozygotes in gnomad4. There are 1822 alleles in male gnomad4 subpopulation. This position pass quality control queck.
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 73 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZSCAN25XR_007059988.1 linkuse as main transcriptn.1429-1315A>T intron_variant, non_coding_transcript_variant
ZSCAN25XR_007059989.1 linkuse as main transcriptn.1371-1315A>T intron_variant, non_coding_transcript_variant
ZSCAN25XR_007059990.1 linkuse as main transcriptn.1244-1315A>T intron_variant, non_coding_transcript_variant
ZSCAN25XR_927402.3 linkuse as main transcriptn.1456-1315A>T 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:
0.0247
AC:
3739
AN:
151408
Hom.:
73
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00914
Gnomad AMI
AF:
0.00768
Gnomad AMR
AF:
0.0268
Gnomad ASJ
AF:
0.0278
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0123
Gnomad FIN
AF:
0.0458
Gnomad MID
AF:
0.0160
Gnomad NFE
AF:
0.0332
Gnomad OTH
AF:
0.0279
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:
0.0247
AC:
3740
AN:
151524
Hom.:
74
Cov.:
31
AF XY:
0.0246
AC XY:
1822
AN XY:
74038
show subpopulations
Gnomad4 AFR
AF:
0.00914
Gnomad4 AMR
AF:
0.0267
Gnomad4 ASJ
AF:
0.0278
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0125
Gnomad4 FIN
AF:
0.0458
Gnomad4 NFE
AF:
0.0332
Gnomad4 OTH
AF:
0.0276
Alfa
AF:
0.0298
Hom.:
13

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
4.8
Dann
Benign
0.42

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: rs45494802; hg19: chr7-99333000; API