3-118473456-T-A

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+23167A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 151,914 control chromosomes in the GnomAD database, including 39,480 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 0.71 ( 39480 hom., cov: 31)

Consequence

ENSG00000243276
ENST00000482142.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.430

Publications

3 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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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
ENSG00000243276ENST00000482142.5 linkn.232+23167A>T intron_variant Intron 3 of 6 5
ENSG00000243276ENST00000833975.1 linkn.448+23167A>T intron_variant Intron 5 of 5
ENSG00000243276ENST00000833976.1 linkn.349+23167A>T intron_variant Intron 4 of 4

Frequencies

GnomAD3 genomes
AF:
0.711
AC:
107932
AN:
151796
Hom.:
39466
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.512
Gnomad AMI
AF:
0.880
Gnomad AMR
AF:
0.741
Gnomad ASJ
AF:
0.761
Gnomad EAS
AF:
0.922
Gnomad SAS
AF:
0.819
Gnomad FIN
AF:
0.760
Gnomad MID
AF:
0.813
Gnomad NFE
AF:
0.788
Gnomad OTH
AF:
0.753
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.711
AC:
107994
AN:
151914
Hom.:
39480
Cov.:
31
AF XY:
0.716
AC XY:
53168
AN XY:
74236
show subpopulations
African (AFR)
AF:
0.511
AC:
21163
AN:
41378
American (AMR)
AF:
0.741
AC:
11312
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.761
AC:
2637
AN:
3466
East Asian (EAS)
AF:
0.922
AC:
4761
AN:
5164
South Asian (SAS)
AF:
0.820
AC:
3942
AN:
4808
European-Finnish (FIN)
AF:
0.760
AC:
8019
AN:
10554
Middle Eastern (MID)
AF:
0.810
AC:
238
AN:
294
European-Non Finnish (NFE)
AF:
0.788
AC:
53529
AN:
67964
Other (OTH)
AF:
0.755
AC:
1590
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1472
2943
4415
5886
7358
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
836
1672
2508
3344
4180
<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:
0.743
Hom.:
5299
Bravo
AF:
0.701
Asia WGS
AF:
0.828
AC:
2880
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.34
DANN
Benign
0.76
PhyloP100
-0.43

Splicing

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

Publications

Other links and lift over

dbSNP: rs12637095; hg19: chr3-118192303; API