rs193741

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 0.815 in 152,086 control chromosomes in the GnomAD database, including 50,680 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 0.82 ( 50680 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62
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=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 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:
0.815
AC:
123924
AN:
151970
Hom.:
50646
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.811
Gnomad AMI
AF:
0.874
Gnomad AMR
AF:
0.776
Gnomad ASJ
AF:
0.804
Gnomad EAS
AF:
0.614
Gnomad SAS
AF:
0.786
Gnomad FIN
AF:
0.849
Gnomad MID
AF:
0.797
Gnomad NFE
AF:
0.840
Gnomad OTH
AF:
0.803
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.815
AC:
124010
AN:
152086
Hom.:
50680
Cov.:
32
AF XY:
0.814
AC XY:
60479
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.811
Gnomad4 AMR
AF:
0.775
Gnomad4 ASJ
AF:
0.804
Gnomad4 EAS
AF:
0.615
Gnomad4 SAS
AF:
0.784
Gnomad4 FIN
AF:
0.849
Gnomad4 NFE
AF:
0.840
Gnomad4 OTH
AF:
0.801
Alfa
AF:
0.832
Hom.:
24470
Bravo
AF:
0.810
Asia WGS
AF:
0.709
AC:
2461
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.21
DANN
Benign
0.48

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: rs193741; hg19: chr5-25692973; API