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GeneBe

rs5743836

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 0.191 in 152,042 control chromosomes in the GnomAD database, including 3,669 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 0.19 ( 3669 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 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:
0.190
AC:
28922
AN:
151924
Hom.:
3665
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.350
Gnomad AMI
AF:
0.189
Gnomad AMR
AF:
0.128
Gnomad ASJ
AF:
0.147
Gnomad EAS
AF:
0.00444
Gnomad SAS
AF:
0.103
Gnomad FIN
AF:
0.0608
Gnomad MID
AF:
0.182
Gnomad NFE
AF:
0.150
Gnomad OTH
AF:
0.198
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.191
AC:
28975
AN:
152042
Hom.:
3669
Cov.:
32
AF XY:
0.183
AC XY:
13630
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.351
Gnomad4 AMR
AF:
0.128
Gnomad4 ASJ
AF:
0.147
Gnomad4 EAS
AF:
0.00445
Gnomad4 SAS
AF:
0.104
Gnomad4 FIN
AF:
0.0608
Gnomad4 NFE
AF:
0.150
Gnomad4 OTH
AF:
0.196
Alfa
AF:
0.196
Hom.:
569
Bravo
AF:
0.203
Asia WGS
AF:
0.0690
AC:
241
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
2.3
Dann
Benign
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs5743836; hg19: chr3-52260782; API