chr1-96034274-T-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The ENST00000766019.1(ENSG00000299748):n.72+4153A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,606 control chromosomes in the GnomAD database, including 11,811 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.39 ( 11811 hom., cov: 32)
Consequence
ENSG00000299748
ENST00000766019.1 intron
ENST00000766019.1 intron
Scores
1
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.90
Publications
13 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 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 |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000299748 | ENST00000766019.1 | n.72+4153A>T | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.388 AC: 58852AN: 151486Hom.: 11801 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
58852
AN:
151486
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.388 AC: 58886AN: 151606Hom.: 11811 Cov.: 32 AF XY: 0.387 AC XY: 28645AN XY: 74088 show subpopulations
GnomAD4 genome
AF:
AC:
58886
AN:
151606
Hom.:
Cov.:
32
AF XY:
AC XY:
28645
AN XY:
74088
show subpopulations
African (AFR)
AF:
AC:
12158
AN:
41344
American (AMR)
AF:
AC:
7287
AN:
15218
Ashkenazi Jewish (ASJ)
AF:
AC:
1383
AN:
3460
East Asian (EAS)
AF:
AC:
2376
AN:
5168
South Asian (SAS)
AF:
AC:
1918
AN:
4822
European-Finnish (FIN)
AF:
AC:
3896
AN:
10570
Middle Eastern (MID)
AF:
AC:
87
AN:
292
European-Non Finnish (NFE)
AF:
AC:
28610
AN:
67718
Other (OTH)
AF:
AC:
814
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1857
3714
5570
7427
9284
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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