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GeneBe

rs16892766

chr8-116618444-A-C

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 0.0914 in 152066 control chromosomes in the gnomAD Genomes database, including 751 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 ( 751 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.26

Links

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BA1
?
GnomAd 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
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;