rs284737

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 0.546 in 152,040 control chromosomes in the GnomAD database, including 25,534 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 0.55 ( 25534 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.378
Variant links:

Genome browser will be placed here

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 = 0.812 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:
0.545
AC:
82826
AN:
151924
Hom.:
25469
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.819
Gnomad AMI
AF:
0.409
Gnomad AMR
AF:
0.532
Gnomad ASJ
AF:
0.423
Gnomad EAS
AF:
0.775
Gnomad SAS
AF:
0.712
Gnomad FIN
AF:
0.404
Gnomad MID
AF:
0.519
Gnomad NFE
AF:
0.383
Gnomad OTH
AF:
0.509
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.546
AC:
82955
AN:
152040
Hom.:
25534
Cov.:
32
AF XY:
0.551
AC XY:
40932
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.820
Gnomad4 AMR
AF:
0.532
Gnomad4 ASJ
AF:
0.423
Gnomad4 EAS
AF:
0.775
Gnomad4 SAS
AF:
0.710
Gnomad4 FIN
AF:
0.404
Gnomad4 NFE
AF:
0.383
Gnomad4 OTH
AF:
0.516
Alfa
AF:
0.424
Hom.:
14331
Bravo
AF:
0.562
Asia WGS
AF:
0.729
AC:
2534
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
1.7
DANN
Benign
0.42

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: rs284737; hg19: chr5-35461200; API