16-49862769-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The variant allele was found at a frequency of 0.0487 in 152,244 control chromosomes in the GnomAD database, including 271 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 0.049 ( 271 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.52
Variant links:

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ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.14).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0719 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0487
AC:
7413
AN:
152126
Hom.:
271
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0141
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.0583
Gnomad ASJ
AF:
0.101
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.0114
Gnomad FIN
AF:
0.0372
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0736
Gnomad OTH
AF:
0.0502
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0487
AC:
7413
AN:
152244
Hom.:
271
Cov.:
33
AF XY:
0.0469
AC XY:
3492
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0141
Gnomad4 AMR
AF:
0.0583
Gnomad4 ASJ
AF:
0.101
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0114
Gnomad4 FIN
AF:
0.0372
Gnomad4 NFE
AF:
0.0736
Gnomad4 OTH
AF:
0.0497
Alfa
AF:
0.0686
Hom.:
631
Bravo
AF:
0.0501
Asia WGS
AF:
0.00664
AC:
24
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.14
CADD
Benign
21
DANN
Benign
0.73

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: rs8058644; hg19: chr16-49896680; API