rs932026

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 0.137 in 152,100 control chromosomes in the GnomAD database, including 1,852 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 0.14 ( 1852 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.128
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 (AFR) allele frequency at 95% confidence interval = 0.237 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:
0.137
AC:
20888
AN:
151982
Hom.:
1849
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.241
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.104
Gnomad EAS
AF:
0.179
Gnomad SAS
AF:
0.177
Gnomad FIN
AF:
0.0337
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0874
Gnomad OTH
AF:
0.149
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.137
AC:
20910
AN:
152100
Hom.:
1852
Cov.:
32
AF XY:
0.134
AC XY:
9987
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.241
Gnomad4 AMR
AF:
0.132
Gnomad4 ASJ
AF:
0.104
Gnomad4 EAS
AF:
0.179
Gnomad4 SAS
AF:
0.178
Gnomad4 FIN
AF:
0.0337
Gnomad4 NFE
AF:
0.0873
Gnomad4 OTH
AF:
0.148
Alfa
AF:
0.102
Hom.:
1246
Bravo
AF:
0.148
Asia WGS
AF:
0.193
AC:
673
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
2.4
DANN
Benign
0.55

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: rs932026; hg19: chr18-36005511; API