chr16-27365589-T-C

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 0.51 in 151,636 control chromosomes in the GnomAD database, including 21,625 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 0.51 ( 21625 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.759
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 (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.510
AC:
77214
AN:
151518
Hom.:
21577
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.767
Gnomad AMI
AF:
0.607
Gnomad AMR
AF:
0.435
Gnomad ASJ
AF:
0.389
Gnomad EAS
AF:
0.532
Gnomad SAS
AF:
0.442
Gnomad FIN
AF:
0.396
Gnomad MID
AF:
0.551
Gnomad NFE
AF:
0.396
Gnomad OTH
AF:
0.461
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.510
AC:
77327
AN:
151636
Hom.:
21625
Cov.:
32
AF XY:
0.508
AC XY:
37685
AN XY:
74138
show subpopulations
Gnomad4 AFR
AF:
0.767
Gnomad4 AMR
AF:
0.436
Gnomad4 ASJ
AF:
0.389
Gnomad4 EAS
AF:
0.531
Gnomad4 SAS
AF:
0.442
Gnomad4 FIN
AF:
0.396
Gnomad4 NFE
AF:
0.396
Gnomad4 OTH
AF:
0.465
Alfa
AF:
0.480
Hom.:
1798
Bravo
AF:
0.524
Asia WGS
AF:
0.499
AC:
1738
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.99
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: rs3024685; hg19: chr16-27376910; API