16-79627600-C-T

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 0.769 in 152,160 control chromosomes in the GnomAD database, including 45,442 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 0.77 ( 45442 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0700
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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 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:
0.769
AC:
116923
AN:
152042
Hom.:
45410
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.710
Gnomad AMI
AF:
0.731
Gnomad AMR
AF:
0.657
Gnomad ASJ
AF:
0.699
Gnomad EAS
AF:
0.692
Gnomad SAS
AF:
0.786
Gnomad FIN
AF:
0.870
Gnomad MID
AF:
0.753
Gnomad NFE
AF:
0.823
Gnomad OTH
AF:
0.768
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.769
AC:
117000
AN:
152160
Hom.:
45442
Cov.:
33
AF XY:
0.768
AC XY:
57142
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.710
Gnomad4 AMR
AF:
0.656
Gnomad4 ASJ
AF:
0.699
Gnomad4 EAS
AF:
0.692
Gnomad4 SAS
AF:
0.787
Gnomad4 FIN
AF:
0.870
Gnomad4 NFE
AF:
0.823
Gnomad4 OTH
AF:
0.767
Alfa
AF:
0.750
Hom.:
2655
Bravo
AF:
0.745
Asia WGS
AF:
0.757
AC:
2634
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.6
DANN
Benign
0.66

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: rs250141; hg19: chr16-79661497; API