16-79655030-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 0.419 in 152,012 control chromosomes in the GnomAD database, including 14,397 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 0.42 ( 14397 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.526
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 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:
0.420
AC:
63727
AN:
151894
Hom.:
14397
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.262
Gnomad AMI
AF:
0.461
Gnomad AMR
AF:
0.372
Gnomad ASJ
AF:
0.391
Gnomad EAS
AF:
0.406
Gnomad SAS
AF:
0.311
Gnomad FIN
AF:
0.592
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.509
Gnomad OTH
AF:
0.426
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.419
AC:
63740
AN:
152012
Hom.:
14397
Cov.:
32
AF XY:
0.420
AC XY:
31193
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.372
Gnomad4 ASJ
AF:
0.391
Gnomad4 EAS
AF:
0.406
Gnomad4 SAS
AF:
0.310
Gnomad4 FIN
AF:
0.592
Gnomad4 NFE
AF:
0.509
Gnomad4 OTH
AF:
0.426
Alfa
AF:
0.419
Hom.:
2537
Bravo
AF:
0.396
Asia WGS
AF:
0.374
AC:
1299
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.5
DANN
Benign
0.74

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: rs8048408; hg19: chr16-79688927; API