rs2251530

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 0.688 in 152,056 control chromosomes in the GnomAD database, including 36,427 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 0.69 ( 36427 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.324
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=-1.0).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 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:
0.688
AC:
104576
AN:
151938
Hom.:
36403
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.716
Gnomad AMI
AF:
0.673
Gnomad AMR
AF:
0.548
Gnomad ASJ
AF:
0.749
Gnomad EAS
AF:
0.496
Gnomad SAS
AF:
0.563
Gnomad FIN
AF:
0.685
Gnomad MID
AF:
0.769
Gnomad NFE
AF:
0.724
Gnomad OTH
AF:
0.691
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.688
AC:
104640
AN:
152056
Hom.:
36427
Cov.:
32
AF XY:
0.681
AC XY:
50648
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.716
Gnomad4 AMR
AF:
0.547
Gnomad4 ASJ
AF:
0.749
Gnomad4 EAS
AF:
0.496
Gnomad4 SAS
AF:
0.562
Gnomad4 FIN
AF:
0.685
Gnomad4 NFE
AF:
0.724
Gnomad4 OTH
AF:
0.694
Alfa
AF:
0.713
Hom.:
52031
Bravo
AF:
0.681
Asia WGS
AF:
0.570
AC:
1981
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.95
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: rs2251530; hg19: chr9-86812940; API