5-99833655-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 0.737 in 151,684 control chromosomes in the GnomAD database, including 41,373 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 0.74 ( 41373 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.553
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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 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:
0.736
AC:
111611
AN:
151566
Hom.:
41327
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.830
Gnomad AMI
AF:
0.645
Gnomad AMR
AF:
0.721
Gnomad ASJ
AF:
0.817
Gnomad EAS
AF:
0.640
Gnomad SAS
AF:
0.724
Gnomad FIN
AF:
0.710
Gnomad MID
AF:
0.816
Gnomad NFE
AF:
0.692
Gnomad OTH
AF:
0.741
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.737
AC:
111716
AN:
151684
Hom.:
41373
Cov.:
30
AF XY:
0.737
AC XY:
54626
AN XY:
74124
show subpopulations
Gnomad4 AFR
AF:
0.830
Gnomad4 AMR
AF:
0.721
Gnomad4 ASJ
AF:
0.817
Gnomad4 EAS
AF:
0.640
Gnomad4 SAS
AF:
0.726
Gnomad4 FIN
AF:
0.710
Gnomad4 NFE
AF:
0.692
Gnomad4 OTH
AF:
0.742
Alfa
AF:
0.711
Hom.:
9591
Bravo
AF:
0.742
Asia WGS
AF:
0.711
AC:
2474
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.89
DANN
Benign
0.70

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: rs6888673; hg19: chr5-99169359; API