ENST00000766019.1:n.72+4153A>T

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

Scores

1
1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.90

Publications

13 publications found
Variant links:
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
ENSG00000299748ENST00000766019.1 linkn.72+4153A>T intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.388
AC:
58852
AN:
151486
Hom.:
11801
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.295
Gnomad AMI
AF:
0.391
Gnomad AMR
AF:
0.478
Gnomad ASJ
AF:
0.400
Gnomad EAS
AF:
0.459
Gnomad SAS
AF:
0.397
Gnomad FIN
AF:
0.369
Gnomad MID
AF:
0.299
Gnomad NFE
AF:
0.422
Gnomad OTH
AF:
0.385
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.388
AC:
58886
AN:
151606
Hom.:
11811
Cov.:
32
AF XY:
0.387
AC XY:
28645
AN XY:
74088
show subpopulations
African (AFR)
AF:
0.294
AC:
12158
AN:
41344
American (AMR)
AF:
0.479
AC:
7287
AN:
15218
Ashkenazi Jewish (ASJ)
AF:
0.400
AC:
1383
AN:
3460
East Asian (EAS)
AF:
0.460
AC:
2376
AN:
5168
South Asian (SAS)
AF:
0.398
AC:
1918
AN:
4822
European-Finnish (FIN)
AF:
0.369
AC:
3896
AN:
10570
Middle Eastern (MID)
AF:
0.298
AC:
87
AN:
292
European-Non Finnish (NFE)
AF:
0.422
AC:
28610
AN:
67718
Other (OTH)
AF:
0.387
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
564
1128
1692
2256
2820
<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:
0.386
Hom.:
1459
Bravo
AF:
0.393

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
-0.080
CADD
Benign
19
DANN
Benign
0.79
PhyloP100
1.9

Splicing

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

Publications

Other links and lift over

dbSNP: rs161115; hg19: chr1-96499830; API