rs9832314

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000810549.1(ENSG00000305353):​n.412+9764A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0634 in 152,306 control chromosomes in the GnomAD database, including 467 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 0.063 ( 467 hom., cov: 32)

Consequence

ENSG00000305353
ENST00000810549.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.94

Publications

4 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 -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 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
ENSG00000305353ENST00000810549.1 linkn.412+9764A>G intron_variant Intron 2 of 2
ENSG00000305353ENST00000810550.1 linkn.371+9764A>G intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.0634
AC:
9652
AN:
152188
Hom.:
464
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0435
Gnomad AMI
AF:
0.0485
Gnomad AMR
AF:
0.0607
Gnomad ASJ
AF:
0.0291
Gnomad EAS
AF:
0.202
Gnomad SAS
AF:
0.143
Gnomad FIN
AF:
0.115
Gnomad MID
AF:
0.0223
Gnomad NFE
AF:
0.0541
Gnomad OTH
AF:
0.0630
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0634
AC:
9662
AN:
152306
Hom.:
467
Cov.:
32
AF XY:
0.0688
AC XY:
5125
AN XY:
74466
show subpopulations
African (AFR)
AF:
0.0436
AC:
1814
AN:
41576
American (AMR)
AF:
0.0604
AC:
924
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
0.0291
AC:
101
AN:
3470
East Asian (EAS)
AF:
0.203
AC:
1053
AN:
5184
South Asian (SAS)
AF:
0.142
AC:
686
AN:
4822
European-Finnish (FIN)
AF:
0.115
AC:
1217
AN:
10610
Middle Eastern (MID)
AF:
0.0274
AC:
8
AN:
292
European-Non Finnish (NFE)
AF:
0.0541
AC:
3679
AN:
68024
Other (OTH)
AF:
0.0643
AC:
136
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
457
914
1370
1827
2284
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
122
244
366
488
610
<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:
0.0629
Hom.:
58
Bravo
AF:
0.0567
Asia WGS
AF:
0.189
AC:
658
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.27
CADD
Benign
16
DANN
Benign
0.81
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: rs9832314; hg19: chr3-72518040; API