chr16-50385293-C-A

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 0.283 in 151,960 control chromosomes in the GnomAD database, including 8,463 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 0.28 ( 8463 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.98
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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:
0.283
AC:
42986
AN:
151842
Hom.:
8469
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.509
Gnomad AMI
AF:
0.223
Gnomad AMR
AF:
0.234
Gnomad ASJ
AF:
0.0893
Gnomad EAS
AF:
0.729
Gnomad SAS
AF:
0.280
Gnomad FIN
AF:
0.237
Gnomad MID
AF:
0.0892
Gnomad NFE
AF:
0.143
Gnomad OTH
AF:
0.237
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.283
AC:
43004
AN:
151960
Hom.:
8463
Cov.:
31
AF XY:
0.288
AC XY:
21398
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.509
Gnomad4 AMR
AF:
0.234
Gnomad4 ASJ
AF:
0.0893
Gnomad4 EAS
AF:
0.729
Gnomad4 SAS
AF:
0.278
Gnomad4 FIN
AF:
0.237
Gnomad4 NFE
AF:
0.143
Gnomad4 OTH
AF:
0.237
Alfa
AF:
0.179
Hom.:
1671
Bravo
AF:
0.295
Asia WGS
AF:
0.477
AC:
1661
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.30
DANN
Benign
0.52

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: rs8054797; hg19: chr16-50419204; API