rs2553827

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 0.59 in 152,038 control chromosomes in the GnomAD database, including 26,741 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 0.59 ( 26741 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06
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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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:
0.590
AC:
89646
AN:
151922
Hom.:
26718
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.589
Gnomad AMI
AF:
0.569
Gnomad AMR
AF:
0.637
Gnomad ASJ
AF:
0.637
Gnomad EAS
AF:
0.786
Gnomad SAS
AF:
0.781
Gnomad FIN
AF:
0.539
Gnomad MID
AF:
0.685
Gnomad NFE
AF:
0.556
Gnomad OTH
AF:
0.617
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.590
AC:
89710
AN:
152038
Hom.:
26741
Cov.:
33
AF XY:
0.595
AC XY:
44247
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.589
Gnomad4 AMR
AF:
0.637
Gnomad4 ASJ
AF:
0.637
Gnomad4 EAS
AF:
0.785
Gnomad4 SAS
AF:
0.780
Gnomad4 FIN
AF:
0.539
Gnomad4 NFE
AF:
0.556
Gnomad4 OTH
AF:
0.620
Alfa
AF:
0.562
Hom.:
2895
Bravo
AF:
0.593
Asia WGS
AF:
0.756
AC:
2621
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.18
DANN
Benign
0.45

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: rs2553827; hg19: chr11-35096667; API