8-27064595-T-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000517322.1(ENSG00000253899):n.684A>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0644 in 152,752 control chromosomes in the GnomAD database, including 471 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 0.065 ( 471 hom., cov: 33)
Exomes 𝑓: 0.025 ( 0 hom. )
Consequence
ENSG00000253899
ENST00000517322.1 non_coding_transcript_exon
ENST00000517322.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.28
Publications
1 publications found
Genes affected
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=-0.58).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000253899 | ENST00000517322.1 | n.684A>T | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes 0.0645 AC: 9815AN: 152202Hom.: 471 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
9815
AN:
152202
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0255 AC: 11AN: 432Hom.: 0 Cov.: 0 AF XY: 0.0308 AC XY: 8AN XY: 260 show subpopulations
GnomAD4 exome
AF:
AC:
11
AN:
432
Hom.:
Cov.:
0
AF XY:
AC XY:
8
AN XY:
260
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
11
AN:
426
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
2
Other (OTH)
AF:
AC:
0
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0645 AC: 9830AN: 152320Hom.: 471 Cov.: 33 AF XY: 0.0614 AC XY: 4572AN XY: 74486 show subpopulations
GnomAD4 genome
AF:
AC:
9830
AN:
152320
Hom.:
Cov.:
33
AF XY:
AC XY:
4572
AN XY:
74486
show subpopulations
African (AFR)
AF:
AC:
5071
AN:
41556
American (AMR)
AF:
AC:
795
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
382
AN:
3472
East Asian (EAS)
AF:
AC:
1
AN:
5192
South Asian (SAS)
AF:
AC:
89
AN:
4824
European-Finnish (FIN)
AF:
AC:
107
AN:
10624
Middle Eastern (MID)
AF:
AC:
27
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3204
AN:
68028
Other (OTH)
AF:
AC:
142
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
468
935
1403
1870
2338
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
104
208
312
416
520
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
49
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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