rs9616906

Variant summary

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

The ENST00000778025.1(ENSG00000301328):​n.40-1275C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,972 control chromosomes in the GnomAD database, including 11,498 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 0.38 ( 11498 hom., cov: 31)

Consequence

ENSG00000301328
ENST00000778025.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.262

Publications

13 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 = 0.444 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
ENSG00000301328ENST00000778025.1 linkn.40-1275C>T intron_variant Intron 1 of 1
ENSG00000301328ENST00000778026.1 linkn.42-1275C>T intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.376
AC:
57029
AN:
151854
Hom.:
11499
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.287
Gnomad AMI
AF:
0.455
Gnomad AMR
AF:
0.322
Gnomad ASJ
AF:
0.620
Gnomad EAS
AF:
0.0717
Gnomad SAS
AF:
0.292
Gnomad FIN
AF:
0.418
Gnomad MID
AF:
0.494
Gnomad NFE
AF:
0.449
Gnomad OTH
AF:
0.413
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.375
AC:
57030
AN:
151972
Hom.:
11498
Cov.:
31
AF XY:
0.368
AC XY:
27362
AN XY:
74268
show subpopulations
African (AFR)
AF:
0.287
AC:
11902
AN:
41442
American (AMR)
AF:
0.321
AC:
4906
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.620
AC:
2151
AN:
3472
East Asian (EAS)
AF:
0.0719
AC:
372
AN:
5176
South Asian (SAS)
AF:
0.290
AC:
1398
AN:
4822
European-Finnish (FIN)
AF:
0.418
AC:
4409
AN:
10554
Middle Eastern (MID)
AF:
0.486
AC:
142
AN:
292
European-Non Finnish (NFE)
AF:
0.449
AC:
30476
AN:
67936
Other (OTH)
AF:
0.408
AC:
860
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1737
3473
5210
6946
8683
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
540
1080
1620
2160
2700
<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:
0.417
Hom.:
36482
Bravo
AF:
0.363
Asia WGS
AF:
0.195
AC:
678
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
1.8
DANN
Benign
0.49
PhyloP100
-0.26

Splicing

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

Publications

Other links and lift over

dbSNP: rs9616906; hg19: chr22-51104680; API