16-59360890-T-G

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 0.103 in 152,216 control chromosomes in the GnomAD database, including 1,584 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 0.10 ( 1584 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.241
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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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:
0.103
AC:
15650
AN:
152098
Hom.:
1583
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.214
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0746
Gnomad ASJ
AF:
0.0458
Gnomad EAS
AF:
0.396
Gnomad SAS
AF:
0.229
Gnomad FIN
AF:
0.0399
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0250
Gnomad OTH
AF:
0.0947
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.103
AC:
15670
AN:
152216
Hom.:
1584
Cov.:
32
AF XY:
0.107
AC XY:
7949
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.214
Gnomad4 AMR
AF:
0.0747
Gnomad4 ASJ
AF:
0.0458
Gnomad4 EAS
AF:
0.396
Gnomad4 SAS
AF:
0.228
Gnomad4 FIN
AF:
0.0399
Gnomad4 NFE
AF:
0.0251
Gnomad4 OTH
AF:
0.0956
Alfa
AF:
0.0690
Hom.:
149
Bravo
AF:
0.110
Asia WGS
AF:
0.264
AC:
919
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
9.0
DANN
Benign
0.64

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: rs17258247; hg19: chr16-59394794; API