rs13332653

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.114 in 152,294 control chromosomes in the GnomAD database, including 1,044 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 0.11 ( 1044 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.369
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.114
AC:
17417
AN:
152176
Hom.:
1046
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0888
Gnomad AMI
AF:
0.115
Gnomad AMR
AF:
0.116
Gnomad ASJ
AF:
0.0827
Gnomad EAS
AF:
0.0786
Gnomad SAS
AF:
0.142
Gnomad FIN
AF:
0.108
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.132
Gnomad OTH
AF:
0.139
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.114
AC:
17418
AN:
152294
Hom.:
1044
Cov.:
32
AF XY:
0.115
AC XY:
8580
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.0889
Gnomad4 AMR
AF:
0.116
Gnomad4 ASJ
AF:
0.0827
Gnomad4 EAS
AF:
0.0786
Gnomad4 SAS
AF:
0.141
Gnomad4 FIN
AF:
0.108
Gnomad4 NFE
AF:
0.132
Gnomad4 OTH
AF:
0.137
Alfa
AF:
0.128
Hom.:
1295
Bravo
AF:
0.114
Asia WGS
AF:
0.104
AC:
362
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
6.8
DANN
Benign
0.74

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13332653; hg19: chr16-24589399; API