rs16822551

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 0.137 in 152,178 control chromosomes in the GnomAD database, including 1,729 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 0.14 ( 1729 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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:
0.137
AC:
20758
AN:
152060
Hom.:
1724
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.220
Gnomad AMI
AF:
0.147
Gnomad AMR
AF:
0.162
Gnomad ASJ
AF:
0.122
Gnomad EAS
AF:
0.170
Gnomad SAS
AF:
0.165
Gnomad FIN
AF:
0.0641
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0880
Gnomad OTH
AF:
0.131
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.137
AC:
20798
AN:
152178
Hom.:
1729
Cov.:
32
AF XY:
0.136
AC XY:
10134
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.220
Gnomad4 AMR
AF:
0.162
Gnomad4 ASJ
AF:
0.122
Gnomad4 EAS
AF:
0.170
Gnomad4 SAS
AF:
0.165
Gnomad4 FIN
AF:
0.0641
Gnomad4 NFE
AF:
0.0880
Gnomad4 OTH
AF:
0.129
Alfa
AF:
0.118
Hom.:
242
Bravo
AF:
0.151
Asia WGS
AF:
0.148
AC:
514
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.23
DANN
Benign
0.53

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: rs16822551; hg19: chr2-227581580; API