5-153260117-A-G

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 0.768 in 151,772 control chromosomes in the GnomAD database, including 48,581 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 0.77 ( 48581 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.502
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 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:
0.769
AC:
116578
AN:
151654
Hom.:
48576
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.416
Gnomad AMI
AF:
0.925
Gnomad AMR
AF:
0.862
Gnomad ASJ
AF:
0.900
Gnomad EAS
AF:
0.707
Gnomad SAS
AF:
0.908
Gnomad FIN
AF:
0.918
Gnomad MID
AF:
0.842
Gnomad NFE
AF:
0.924
Gnomad OTH
AF:
0.779
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.768
AC:
116617
AN:
151772
Hom.:
48581
Cov.:
31
AF XY:
0.772
AC XY:
57267
AN XY:
74200
show subpopulations
Gnomad4 AFR
AF:
0.416
Gnomad4 AMR
AF:
0.862
Gnomad4 ASJ
AF:
0.900
Gnomad4 EAS
AF:
0.708
Gnomad4 SAS
AF:
0.908
Gnomad4 FIN
AF:
0.918
Gnomad4 NFE
AF:
0.924
Gnomad4 OTH
AF:
0.777
Alfa
AF:
0.903
Hom.:
57611
Bravo
AF:
0.745
Asia WGS
AF:
0.773
AC:
2687
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.7
DANN
Benign
0.23

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: rs3112530; hg19: chr5-152639677; COSMIC: COSV60214316; API