ENST00000521472.6:n.289+2201G>A

Variant summary

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

The ENST00000521472.6(ENSG00000249738):​n.289+2201G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,210 control chromosomes in the GnomAD database, including 1,951 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 0.15 ( 1951 hom., cov: 32)

Consequence

ENSG00000249738
ENST00000521472.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.398

Publications

24 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=-0.77).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105377683XR_941138.3 linkn.401-1603G>A intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000249738ENST00000521472.6 linkn.289+2201G>A intron_variant Intron 2 of 3 3
ENSG00000249738ENST00000764992.1 linkn.380+2201G>A intron_variant Intron 2 of 4
ENSG00000249738ENST00000765003.1 linkn.387+2201G>A intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.150
AC:
22860
AN:
152092
Hom.:
1947
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0749
Gnomad AMI
AF:
0.109
Gnomad AMR
AF:
0.127
Gnomad ASJ
AF:
0.213
Gnomad EAS
AF:
0.172
Gnomad SAS
AF:
0.120
Gnomad FIN
AF:
0.249
Gnomad MID
AF:
0.180
Gnomad NFE
AF:
0.184
Gnomad OTH
AF:
0.161
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.150
AC:
22872
AN:
152210
Hom.:
1951
Cov.:
32
AF XY:
0.152
AC XY:
11340
AN XY:
74422
show subpopulations
African (AFR)
AF:
0.0749
AC:
3109
AN:
41530
American (AMR)
AF:
0.127
AC:
1937
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.213
AC:
739
AN:
3472
East Asian (EAS)
AF:
0.173
AC:
896
AN:
5190
South Asian (SAS)
AF:
0.120
AC:
577
AN:
4826
European-Finnish (FIN)
AF:
0.249
AC:
2633
AN:
10582
Middle Eastern (MID)
AF:
0.177
AC:
52
AN:
294
European-Non Finnish (NFE)
AF:
0.184
AC:
12482
AN:
68002
Other (OTH)
AF:
0.165
AC:
348
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1025
2050
3074
4099
5124
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
260
520
780
1040
1300
<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:
0.168
Hom.:
2970
Bravo
AF:
0.140
Asia WGS
AF:
0.150
AC:
521
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
4.3
DANN
Benign
0.69
PhyloP100
0.40

Splicing

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

Publications

Other links and lift over

dbSNP: rs3181225; hg19: chr5-158740623; API