5-28212616-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 0.58 in 152,026 control chromosomes in the GnomAD database, including 30,350 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 0.58 ( 30350 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.107
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 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:
0.581
AC:
88271
AN:
151910
Hom.:
30361
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.209
Gnomad AMI
AF:
0.777
Gnomad AMR
AF:
0.619
Gnomad ASJ
AF:
0.755
Gnomad EAS
AF:
0.320
Gnomad SAS
AF:
0.726
Gnomad FIN
AF:
0.765
Gnomad MID
AF:
0.725
Gnomad NFE
AF:
0.766
Gnomad OTH
AF:
0.646
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.580
AC:
88243
AN:
152026
Hom.:
30350
Cov.:
33
AF XY:
0.583
AC XY:
43370
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.208
Gnomad4 AMR
AF:
0.618
Gnomad4 ASJ
AF:
0.755
Gnomad4 EAS
AF:
0.320
Gnomad4 SAS
AF:
0.725
Gnomad4 FIN
AF:
0.765
Gnomad4 NFE
AF:
0.766
Gnomad4 OTH
AF:
0.640
Alfa
AF:
0.626
Hom.:
7229
Bravo
AF:
0.549
Asia WGS
AF:
0.514
AC:
1771
AN:
3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
3.5
DANN
Benign
0.43

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: rs7727623; hg19: chr5-28212723; API