rs9380062

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000562227.2(ZKSCAN8P1):​c.*576G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,972 control chromosomes in the GnomAD database, including 4,142 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 0.23 ( 4142 hom., cov: 32)

Consequence

ZKSCAN8P1
ENST00000562227.2 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.552
Variant links:
Genes affected
ZKSCAN8P1 (HGNC:18777): (ZKSCAN8 pseudogene 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZKSCAN8P1NR_103448.1 linkn.*196G>A downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZKSCAN8P1ENST00000562227.2 linkc.*576G>A downstream_gene_variant 3 ENSP00000510811.1 A0A8I5KTY6
ZKSCAN8P1ENST00000440790.6 linkc.*576G>A downstream_gene_variant 5 ENSP00000509393.1 A0A8I5KTY6

Frequencies

GnomAD3 genomes
AF:
0.229
AC:
34820
AN:
151854
Hom.:
4135
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.284
Gnomad AMI
AF:
0.291
Gnomad AMR
AF:
0.241
Gnomad ASJ
AF:
0.168
Gnomad EAS
AF:
0.175
Gnomad SAS
AF:
0.140
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.214
Gnomad OTH
AF:
0.222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.229
AC:
34856
AN:
151972
Hom.:
4142
Cov.:
32
AF XY:
0.224
AC XY:
16622
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.283
Gnomad4 AMR
AF:
0.241
Gnomad4 ASJ
AF:
0.168
Gnomad4 EAS
AF:
0.175
Gnomad4 SAS
AF:
0.142
Gnomad4 FIN
AF:
0.183
Gnomad4 NFE
AF:
0.214
Gnomad4 OTH
AF:
0.220
Alfa
AF:
0.222
Hom.:
1384
Bravo
AF:
0.240
Asia WGS
AF:
0.154
AC:
537
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.58
DANN
Benign
0.80

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: rs9380062; hg19: chr6-28137569; API