10-75262703-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000734866.1(ZNF503-AS1):​n.17C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 122,022 control chromosomes in the GnomAD database, including 459 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 0.082 ( 459 hom., cov: 28)

Consequence

ZNF503-AS1
ENST00000734866.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.11

Publications

1 publications found
Variant links:
Genes affected
ZNF503-AS1 (HGNC:27370): (ZNF503 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF503-AS1ENST00000734866.1 linkn.17C>T non_coding_transcript_exon_variant Exon 1 of 3
ZNF503-AS1ENST00000666247.1 linkn.291+17267C>T intron_variant Intron 2 of 3
ZNF503-AS1ENST00000734865.1 linkn.311+17267C>T intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.0820
AC:
10005
AN:
121998
Hom.:
457
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.0316
Gnomad AMI
AF:
0.0495
Gnomad AMR
AF:
0.114
Gnomad ASJ
AF:
0.0940
Gnomad EAS
AF:
0.0558
Gnomad SAS
AF:
0.275
Gnomad FIN
AF:
0.0542
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.0933
Gnomad OTH
AF:
0.108
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0820
AC:
10005
AN:
122022
Hom.:
459
Cov.:
28
AF XY:
0.0868
AC XY:
4896
AN XY:
56378
show subpopulations
African (AFR)
AF:
0.0316
AC:
999
AN:
31624
American (AMR)
AF:
0.114
AC:
1078
AN:
9434
Ashkenazi Jewish (ASJ)
AF:
0.0940
AC:
311
AN:
3308
East Asian (EAS)
AF:
0.0557
AC:
191
AN:
3432
South Asian (SAS)
AF:
0.275
AC:
1052
AN:
3832
European-Finnish (FIN)
AF:
0.0542
AC:
255
AN:
4708
Middle Eastern (MID)
AF:
0.143
AC:
26
AN:
182
European-Non Finnish (NFE)
AF:
0.0932
AC:
5868
AN:
62942
Other (OTH)
AF:
0.108
AC:
182
AN:
1692
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
432
865
1297
1730
2162
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
128
256
384
512
640
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0774
Hom.:
849
Bravo
AF:
0.0647

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.016
DANN
Benign
0.80
PhyloP100
-2.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs12766938; hg19: chr10-77022461; API