rs2551691

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 0.837 in 152,174 control chromosomes in the GnomAD database, including 53,825 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 0.84 ( 53825 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0180
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.838
AC:
127372
AN:
152054
Hom.:
53804
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.713
Gnomad AMI
AF:
0.732
Gnomad AMR
AF:
0.879
Gnomad ASJ
AF:
0.842
Gnomad EAS
AF:
0.996
Gnomad SAS
AF:
0.866
Gnomad FIN
AF:
0.859
Gnomad MID
AF:
0.790
Gnomad NFE
AF:
0.889
Gnomad OTH
AF:
0.826
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.837
AC:
127420
AN:
152174
Hom.:
53825
Cov.:
32
AF XY:
0.837
AC XY:
62315
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.712
Gnomad4 AMR
AF:
0.879
Gnomad4 ASJ
AF:
0.842
Gnomad4 EAS
AF:
0.996
Gnomad4 SAS
AF:
0.866
Gnomad4 FIN
AF:
0.859
Gnomad4 NFE
AF:
0.889
Gnomad4 OTH
AF:
0.828
Alfa
AF:
0.879
Hom.:
68223
Bravo
AF:
0.836
Asia WGS
AF:
0.913
AC:
3173
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.9
DANN
Benign
0.70

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: rs2551691; hg19: chr2-161889193; API