5-150164482-G-A

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 0.482 in 151,816 control chromosomes in the GnomAD database, including 17,954 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 0.48 ( 17954 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.86
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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:
0.482
AC:
73124
AN:
151698
Hom.:
17930
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.563
Gnomad AMI
AF:
0.569
Gnomad AMR
AF:
0.437
Gnomad ASJ
AF:
0.627
Gnomad EAS
AF:
0.550
Gnomad SAS
AF:
0.476
Gnomad FIN
AF:
0.377
Gnomad MID
AF:
0.630
Gnomad NFE
AF:
0.444
Gnomad OTH
AF:
0.511
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.482
AC:
73189
AN:
151816
Hom.:
17954
Cov.:
31
AF XY:
0.479
AC XY:
35542
AN XY:
74192
show subpopulations
Gnomad4 AFR
AF:
0.563
Gnomad4 AMR
AF:
0.438
Gnomad4 ASJ
AF:
0.627
Gnomad4 EAS
AF:
0.550
Gnomad4 SAS
AF:
0.477
Gnomad4 FIN
AF:
0.377
Gnomad4 NFE
AF:
0.444
Gnomad4 OTH
AF:
0.508
Alfa
AF:
0.455
Hom.:
20445
Bravo
AF:
0.488
Asia WGS
AF:
0.505
AC:
1758
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.46
DANN
Benign
0.28

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: rs3776082; hg19: chr5-149544045; API