GeneBe

16-72722202-G-T

Variant names:

Variant summary

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

The ENST00000563328.5(ZFHX3-AS1):​n.203-23203G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,096 control chromosomes in the GnomAD database, including 3,628 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 0.19 ( 3628 hom., cov: 32)

Consequence

ZFHX3-AS1
ENST00000563328.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.414

Publications

9 publications found
Variant links:
Genes affected
ZFHX3-AS1 (HGNC:56033): (ZFHX3 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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZFHX3-AS1NR_171702.1 linkn.328+8213G>T intron_variant Intron 3 of 4
ZFHX3-AS1NR_171703.1 linkn.285+8786G>T intron_variant Intron 2 of 4
ZFHX3-AS1NR_171704.1 linkn.285+8786G>T intron_variant Intron 2 of 3
ZFHX3-AS1NR_171705.1 linkn.202-23203G>T intron_variant Intron 1 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZFHX3-AS1ENST00000563328.5 linkn.203-23203G>T intron_variant Intron 1 of 4 3
ZFHX3-AS1ENST00000653037.2 linkn.290+8786G>T intron_variant Intron 2 of 4
ZFHX3-AS1ENST00000668995.1 linkn.338+8213G>T intron_variant Intron 3 of 4

Frequencies

GnomAD3 genomes
AF:
0.191
AC:
29061
AN:
151978
Hom.:
3628
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0530
Gnomad AMI
AF:
0.209
Gnomad AMR
AF:
0.167
Gnomad ASJ
AF:
0.272
Gnomad EAS
AF:
0.0285
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.225
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.289
Gnomad OTH
AF:
0.201
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.191
AC:
29053
AN:
152096
Hom.:
3628
Cov.:
32
AF XY:
0.187
AC XY:
13883
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.0529
AC:
2197
AN:
41538
American (AMR)
AF:
0.167
AC:
2551
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.272
AC:
942
AN:
3464
East Asian (EAS)
AF:
0.0288
AC:
149
AN:
5182
South Asian (SAS)
AF:
0.108
AC:
523
AN:
4822
European-Finnish (FIN)
AF:
0.225
AC:
2376
AN:
10552
Middle Eastern (MID)
AF:
0.218
AC:
64
AN:
294
European-Non Finnish (NFE)
AF:
0.289
AC:
19640
AN:
67946
Other (OTH)
AF:
0.199
AC:
420
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1109
2217
3326
4434
5543
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
302
604
906
1208
1510
<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:
0.243
Hom.:
10437
Bravo
AF:
0.181
Asia WGS
AF:
0.0750
AC:
264
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
4.3
DANN
Benign
0.70
PhyloP100
0.41

Splicing

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

Publications

Other links and lift over

dbSNP: rs10500569; hg19: chr16-72756101; API