rs16832011

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 0.0489 in 156,138 control chromosomes in the GnomAD database, including 346 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 0.050 ( 345 hom., cov: 32)
Exomes 𝑓: 0.013 ( 1 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.171
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0498
AC:
7580
AN:
152118
Hom.:
346
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.117
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0324
Gnomad ASJ
AF:
0.0305
Gnomad EAS
AF:
0.0591
Gnomad SAS
AF:
0.0168
Gnomad FIN
AF:
0.0135
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.0224
Gnomad OTH
AF:
0.0407
GnomAD4 exome
AF:
0.0131
AC:
51
AN:
3902
Hom.:
1
AF XY:
0.0141
AC XY:
29
AN XY:
2064
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0167
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0500
Gnomad4 SAS exome
AF:
0.00995
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0114
Gnomad4 OTH exome
AF:
0.00725
GnomAD4 genome
AF:
0.0498
AC:
7587
AN:
152236
Hom.:
345
Cov.:
32
AF XY:
0.0485
AC XY:
3612
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.116
Gnomad4 AMR
AF:
0.0325
Gnomad4 ASJ
AF:
0.0305
Gnomad4 EAS
AF:
0.0592
Gnomad4 SAS
AF:
0.0168
Gnomad4 FIN
AF:
0.0135
Gnomad4 NFE
AF:
0.0224
Gnomad4 OTH
AF:
0.0412
Alfa
AF:
0.0286
Hom.:
182
Bravo
AF:
0.0538
Asia WGS
AF:
0.0320
AC:
111
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
3.2
DANN
Benign
0.43

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: rs16832011; hg19: chr2-136545299; API