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GeneBe

rs16892766

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.0913 in 152,184 control chromosomes in the GnomAD database, including 752 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 0.091 ( 752 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.26
Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 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:
0.0914
AC:
13895
AN:
152066
Hom.:
751
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.127
Gnomad AMI
AF:
0.0725
Gnomad AMR
AF:
0.0592
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.000583
Gnomad SAS
AF:
0.0896
Gnomad FIN
AF:
0.117
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.0776
Gnomad OTH
AF:
0.0903
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0913
AC:
13900
AN:
152184
Hom.:
752
Cov.:
32
AF XY:
0.0924
AC XY:
6870
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.127
Gnomad4 AMR
AF:
0.0591
Gnomad4 ASJ
AF:
0.134
Gnomad4 EAS
AF:
0.000584
Gnomad4 SAS
AF:
0.0898
Gnomad4 FIN
AF:
0.117
Gnomad4 NFE
AF:
0.0776
Gnomad4 OTH
AF:
0.0884
Alfa
AF:
0.0774
Hom.:
1138
Bravo
AF:
0.0879
Asia WGS
AF:
0.0460
AC:
161
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.39
Cadd
Benign
22
Dann
Benign
0.75

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: rs16892766; hg19: chr8-117630683; COSMIC: COSV58902220; API