rs284744

Variant summary

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

The ENST00000824642.1(ENSG00000307231):​n.137-16517T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,206 control chromosomes in the GnomAD database, including 10,462 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 0.33 ( 10462 hom., cov: 33)

Consequence

ENSG00000307231
ENST00000824642.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.161

Publications

1 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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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
ENSG00000307231ENST00000824642.1 linkn.137-16517T>G intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.326
AC:
49640
AN:
152088
Hom.:
10412
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.571
Gnomad AMI
AF:
0.200
Gnomad AMR
AF:
0.349
Gnomad ASJ
AF:
0.168
Gnomad EAS
AF:
0.488
Gnomad SAS
AF:
0.379
Gnomad FIN
AF:
0.153
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.194
Gnomad OTH
AF:
0.302
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.327
AC:
49753
AN:
152206
Hom.:
10462
Cov.:
33
AF XY:
0.328
AC XY:
24389
AN XY:
74430
show subpopulations
African (AFR)
AF:
0.572
AC:
23744
AN:
41498
American (AMR)
AF:
0.350
AC:
5347
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.168
AC:
583
AN:
3472
East Asian (EAS)
AF:
0.488
AC:
2524
AN:
5172
South Asian (SAS)
AF:
0.378
AC:
1825
AN:
4830
European-Finnish (FIN)
AF:
0.153
AC:
1628
AN:
10608
Middle Eastern (MID)
AF:
0.269
AC:
79
AN:
294
European-Non Finnish (NFE)
AF:
0.194
AC:
13191
AN:
68018
Other (OTH)
AF:
0.307
AC:
650
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1548
3096
4643
6191
7739
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
468
936
1404
1872
2340
<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:
0.253
Hom.:
1240
Bravo
AF:
0.352
Asia WGS
AF:
0.436
AC:
1518
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
5.1
DANN
Benign
0.74
PhyloP100
0.16

Splicing

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

Publications

Other links and lift over

dbSNP: rs284744; hg19: chr5-35470288; API