ENST00000827668.1:n.232+37198A>G

Variant summary

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

The ENST00000827668.1(ENSG00000307651):​n.232+37198A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,144 control chromosomes in the GnomAD database, including 4,548 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 0.23 ( 4548 hom., cov: 32)

Consequence

ENSG00000307651
ENST00000827668.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.221

Publications

2 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=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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
ENSG00000307651ENST00000827668.1 linkn.232+37198A>G intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.227
AC:
34453
AN:
152026
Hom.:
4538
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.354
Gnomad AMI
AF:
0.180
Gnomad AMR
AF:
0.169
Gnomad ASJ
AF:
0.189
Gnomad EAS
AF:
0.00231
Gnomad SAS
AF:
0.122
Gnomad FIN
AF:
0.179
Gnomad MID
AF:
0.187
Gnomad NFE
AF:
0.197
Gnomad OTH
AF:
0.212
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.227
AC:
34495
AN:
152144
Hom.:
4548
Cov.:
32
AF XY:
0.224
AC XY:
16640
AN XY:
74398
show subpopulations
African (AFR)
AF:
0.354
AC:
14668
AN:
41474
American (AMR)
AF:
0.169
AC:
2585
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.189
AC:
656
AN:
3468
East Asian (EAS)
AF:
0.00232
AC:
12
AN:
5178
South Asian (SAS)
AF:
0.122
AC:
589
AN:
4824
European-Finnish (FIN)
AF:
0.179
AC:
1902
AN:
10608
Middle Eastern (MID)
AF:
0.184
AC:
54
AN:
294
European-Non Finnish (NFE)
AF:
0.197
AC:
13421
AN:
67998
Other (OTH)
AF:
0.210
AC:
444
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1299
2598
3897
5196
6495
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
344
688
1032
1376
1720
<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:
0.209
Hom.:
2358
Bravo
AF:
0.231
Asia WGS
AF:
0.0700
AC:
244
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
1.8
DANN
Benign
0.80
PhyloP100
-0.22

Splicing

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

Publications

Other links and lift over

dbSNP: rs11147637; hg19: chr13-37767059; API