rs753013

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 0.424 in 151,956 control chromosomes in the GnomAD database, including 14,487 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 0.42 ( 14487 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.597
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=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.569 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:
0.425
AC:
64479
AN:
151838
Hom.:
14477
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.296
Gnomad AMI
AF:
0.436
Gnomad AMR
AF:
0.578
Gnomad ASJ
AF:
0.474
Gnomad EAS
AF:
0.340
Gnomad SAS
AF:
0.488
Gnomad FIN
AF:
0.510
Gnomad MID
AF:
0.369
Gnomad NFE
AF:
0.455
Gnomad OTH
AF:
0.423
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.424
AC:
64503
AN:
151956
Hom.:
14487
Cov.:
31
AF XY:
0.430
AC XY:
31962
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.296
Gnomad4 AMR
AF:
0.579
Gnomad4 ASJ
AF:
0.474
Gnomad4 EAS
AF:
0.341
Gnomad4 SAS
AF:
0.487
Gnomad4 FIN
AF:
0.510
Gnomad4 NFE
AF:
0.455
Gnomad4 OTH
AF:
0.418
Alfa
AF:
0.430
Hom.:
1775
Bravo
AF:
0.424
Asia WGS
AF:
0.415
AC:
1441
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.5
DANN
Benign
0.66

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: rs753013; hg19: chr12-29052910; API