rs927724

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 0.893 in 152,096 control chromosomes in the GnomAD database, including 60,756 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 0.89 ( 60756 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15
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=-1.05).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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:
0.893
AC:
135770
AN:
151982
Hom.:
60688
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.910
Gnomad AMI
AF:
0.948
Gnomad AMR
AF:
0.910
Gnomad ASJ
AF:
0.866
Gnomad EAS
AF:
0.876
Gnomad SAS
AF:
0.861
Gnomad FIN
AF:
0.902
Gnomad MID
AF:
0.826
Gnomad NFE
AF:
0.883
Gnomad OTH
AF:
0.900
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.893
AC:
135894
AN:
152096
Hom.:
60756
Cov.:
31
AF XY:
0.893
AC XY:
66421
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.910
Gnomad4 AMR
AF:
0.910
Gnomad4 ASJ
AF:
0.866
Gnomad4 EAS
AF:
0.876
Gnomad4 SAS
AF:
0.861
Gnomad4 FIN
AF:
0.902
Gnomad4 NFE
AF:
0.883
Gnomad4 OTH
AF:
0.901
Alfa
AF:
0.884
Hom.:
64108
Bravo
AF:
0.897
Asia WGS
AF:
0.874
AC:
3024
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.51
DANN
Benign
0.24

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: rs927724; hg19: chr1-196174790; API