2-232515231-G-A

Variant summary

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

The variant allele was found at a frequency of 0.175 in 151,968 control chromosomes in the GnomAD database, including 2,466 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 0.18 ( 2466 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.159

Publications

17 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 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

Frequencies

GnomAD3 genomes
AF:
0.175
AC:
26590
AN:
151848
Hom.:
2464
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.198
Gnomad AMI
AF:
0.184
Gnomad AMR
AF:
0.149
Gnomad ASJ
AF:
0.144
Gnomad EAS
AF:
0.0249
Gnomad SAS
AF:
0.144
Gnomad FIN
AF:
0.148
Gnomad MID
AF:
0.172
Gnomad NFE
AF:
0.186
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.175
AC:
26595
AN:
151968
Hom.:
2466
Cov.:
31
AF XY:
0.172
AC XY:
12750
AN XY:
74280
show subpopulations
African (AFR)
AF:
0.198
AC:
8195
AN:
41416
American (AMR)
AF:
0.149
AC:
2271
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.144
AC:
499
AN:
3468
East Asian (EAS)
AF:
0.0251
AC:
130
AN:
5172
South Asian (SAS)
AF:
0.143
AC:
689
AN:
4812
European-Finnish (FIN)
AF:
0.148
AC:
1565
AN:
10574
Middle Eastern (MID)
AF:
0.158
AC:
46
AN:
292
European-Non Finnish (NFE)
AF:
0.186
AC:
12646
AN:
67942
Other (OTH)
AF:
0.184
AC:
387
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1105
2210
3316
4421
5526
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
288
576
864
1152
1440
<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:
0.177
Hom.:
4467
Bravo
AF:
0.175
Asia WGS
AF:
0.103
AC:
361
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
2.3
DANN
Benign
0.61
PhyloP100
0.16

Splicing

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

Publications

Other links and lift over

dbSNP: rs1656404; hg19: chr2-233379941; API