rs729239

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 0.131 in 152,130 control chromosomes in the GnomAD database, including 2,014 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 0.13 ( 2014 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.01
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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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:
0.130
AC:
19823
AN:
152012
Hom.:
2003
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.283
Gnomad AMI
AF:
0.141
Gnomad AMR
AF:
0.0863
Gnomad ASJ
AF:
0.0565
Gnomad EAS
AF:
0.0390
Gnomad SAS
AF:
0.0767
Gnomad FIN
AF:
0.0401
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.0770
Gnomad OTH
AF:
0.111
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.131
AC:
19880
AN:
152130
Hom.:
2014
Cov.:
32
AF XY:
0.126
AC XY:
9396
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.283
Gnomad4 AMR
AF:
0.0861
Gnomad4 ASJ
AF:
0.0565
Gnomad4 EAS
AF:
0.0389
Gnomad4 SAS
AF:
0.0774
Gnomad4 FIN
AF:
0.0401
Gnomad4 NFE
AF:
0.0770
Gnomad4 OTH
AF:
0.113
Alfa
AF:
0.124
Hom.:
309
Bravo
AF:
0.141
Asia WGS
AF:
0.103
AC:
357
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.010
DANN
Benign
0.38

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: rs729239; hg19: chr4-78063396; API