rs2554152

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 0.241 in 152,122 control chromosomes in the GnomAD database, including 6,980 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 0.24 ( 6980 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04
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=-0.77).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 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:
0.241
AC:
36594
AN:
152004
Hom.:
6964
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.536
Gnomad AMI
AF:
0.163
Gnomad AMR
AF:
0.141
Gnomad ASJ
AF:
0.158
Gnomad EAS
AF:
0.221
Gnomad SAS
AF:
0.168
Gnomad FIN
AF:
0.0861
Gnomad MID
AF:
0.171
Gnomad NFE
AF:
0.122
Gnomad OTH
AF:
0.190
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.241
AC:
36639
AN:
152122
Hom.:
6980
Cov.:
32
AF XY:
0.238
AC XY:
17668
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.535
Gnomad4 AMR
AF:
0.141
Gnomad4 ASJ
AF:
0.158
Gnomad4 EAS
AF:
0.221
Gnomad4 SAS
AF:
0.167
Gnomad4 FIN
AF:
0.0861
Gnomad4 NFE
AF:
0.122
Gnomad4 OTH
AF:
0.188
Alfa
AF:
0.143
Hom.:
3426
Bravo
AF:
0.258
Asia WGS
AF:
0.202
AC:
702
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
15
DANN
Benign
0.88

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: rs2554152; hg19: chr3-139606794; API