chr9-114814199-C-T

Variant summary

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

The ENST00000776746.1(ENSG00000301160):​n.454-2197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,856 control chromosomes in the GnomAD database, including 3,249 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 0.19 ( 3249 hom., cov: 32)

Consequence

ENSG00000301160
ENST00000776746.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 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
ENSG00000301160ENST00000776746.1 linkn.454-2197G>A intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.195
AC:
29541
AN:
151738
Hom.:
3245
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.288
Gnomad AMI
AF:
0.209
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.137
Gnomad EAS
AF:
0.194
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.101
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.150
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.195
AC:
29580
AN:
151856
Hom.:
3249
Cov.:
32
AF XY:
0.194
AC XY:
14427
AN XY:
74192
show subpopulations
African (AFR)
AF:
0.288
AC:
11898
AN:
41370
American (AMR)
AF:
0.210
AC:
3211
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.137
AC:
476
AN:
3464
East Asian (EAS)
AF:
0.195
AC:
1002
AN:
5148
South Asian (SAS)
AF:
0.232
AC:
1114
AN:
4794
European-Finnish (FIN)
AF:
0.101
AC:
1068
AN:
10532
Middle Eastern (MID)
AF:
0.167
AC:
49
AN:
294
European-Non Finnish (NFE)
AF:
0.150
AC:
10184
AN:
67962
Other (OTH)
AF:
0.184
AC:
388
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1179
2359
3538
4718
5897
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
316
632
948
1264
1580
<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:
0.183
Hom.:
652
Bravo
AF:
0.203
Asia WGS
AF:
0.210
AC:
730
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.22
DANN
Benign
0.54
PhyloP100
-1.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs7865494; hg19: chr9-117576479; API