6-135689660-A-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000421378.4(AHI1-DT):n.456A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AHI1-DT
ENST00000421378.4 non_coding_transcript_exon
ENST00000421378.4 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.14
Publications
3 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| AHI1-DT | NR_026805.1 | n.458A>T | non_coding_transcript_exon_variant | Exon 4 of 4 | ||||
| AHI1-DT | NR_152842.1 | n.572A>T | non_coding_transcript_exon_variant | Exon 5 of 6 | ||||
| AHI1-DT | NR_152844.1 | n.572A>T | non_coding_transcript_exon_variant | Exon 5 of 5 | ||||
| AHI1-DT | NR_152845.1 | n.696A>T | non_coding_transcript_exon_variant | Exon 5 of 5 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| AHI1-DT | ENST00000421378.4 | n.456A>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 1 | |||||
| AHI1-DT | ENST00000579944.1 | n.154A>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | |||||
| AHI1-DT | ENST00000653664.1 | n.596A>T | non_coding_transcript_exon_variant | Exon 5 of 5 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151762Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
151762
Hom.:
Cov.:
32
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 Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 68Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 44
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
68
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
44
African (AFR)
AF:
AC:
0
AN:
4
American (AMR)
AF:
AC:
0
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
0
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
0
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
54
Other (OTH)
AF:
AC:
0
AN:
4
GnomAD4 genome 0.00 AC: 0AN: 151762Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74080
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
151762
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74080
African (AFR)
AF:
AC:
0
AN:
41276
American (AMR)
AF:
AC:
0
AN:
15230
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5170
South Asian (SAS)
AF:
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
AC:
0
AN:
10542
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67936
Other (OTH)
AF:
AC:
0
AN:
2090
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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