ENST00000524085.2:n.299-8472G>A

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.299-8472G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,098 control chromosomes in the GnomAD database, including 1,336 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 0.12 ( 1336 hom., cov: 32)

Consequence

ENSG00000253374
ENST00000524085.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117

Publications

9 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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC101927118XR_001745980.2 linkn.517+27471G>A intron_variant Intron 1 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000253374ENST00000524085.2 linkn.299-8472G>A intron_variant Intron 2 of 3 5
ENSG00000253374ENST00000832857.1 linkn.327-32262G>A intron_variant Intron 2 of 9
ENSG00000253374ENST00000832858.1 linkn.309-32262G>A intron_variant Intron 2 of 9
ENSG00000253374ENST00000832859.1 linkn.328-32262G>A intron_variant Intron 2 of 5

Frequencies

GnomAD3 genomes
AF:
0.124
AC:
18832
AN:
151980
Hom.:
1333
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0770
Gnomad AMI
AF:
0.0855
Gnomad AMR
AF:
0.0970
Gnomad ASJ
AF:
0.163
Gnomad EAS
AF:
0.00173
Gnomad SAS
AF:
0.143
Gnomad FIN
AF:
0.117
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.166
Gnomad OTH
AF:
0.124
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.124
AC:
18841
AN:
152098
Hom.:
1336
Cov.:
32
AF XY:
0.121
AC XY:
9026
AN XY:
74358
show subpopulations
African (AFR)
AF:
0.0768
AC:
3187
AN:
41496
American (AMR)
AF:
0.0970
AC:
1482
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.163
AC:
564
AN:
3470
East Asian (EAS)
AF:
0.00174
AC:
9
AN:
5178
South Asian (SAS)
AF:
0.145
AC:
698
AN:
4822
European-Finnish (FIN)
AF:
0.117
AC:
1233
AN:
10574
Middle Eastern (MID)
AF:
0.139
AC:
41
AN:
294
European-Non Finnish (NFE)
AF:
0.166
AC:
11291
AN:
67962
Other (OTH)
AF:
0.122
AC:
258
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
848
1695
2543
3390
4238
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
222
444
666
888
1110
<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:
0.142
Hom.:
297
Bravo
AF:
0.117
Asia WGS
AF:
0.0560
AC:
195
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.7
DANN
Benign
0.26
PhyloP100
0.12

Splicing

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

Publications

Other links and lift over

dbSNP: rs16909233; hg19: chr8-82401680; API