rs2204502

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 0.4 in 151,930 control chromosomes in the GnomAD database, including 13,364 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 0.40 ( 13364 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.703
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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 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:
0.400
AC:
60718
AN:
151812
Hom.:
13364
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.237
Gnomad AMI
AF:
0.458
Gnomad AMR
AF:
0.353
Gnomad ASJ
AF:
0.443
Gnomad EAS
AF:
0.207
Gnomad SAS
AF:
0.440
Gnomad FIN
AF:
0.424
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.515
Gnomad OTH
AF:
0.413
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.400
AC:
60719
AN:
151930
Hom.:
13364
Cov.:
31
AF XY:
0.393
AC XY:
29202
AN XY:
74234
show subpopulations
Gnomad4 AFR
AF:
0.237
Gnomad4 AMR
AF:
0.353
Gnomad4 ASJ
AF:
0.443
Gnomad4 EAS
AF:
0.207
Gnomad4 SAS
AF:
0.440
Gnomad4 FIN
AF:
0.424
Gnomad4 NFE
AF:
0.515
Gnomad4 OTH
AF:
0.409
Alfa
AF:
0.481
Hom.:
36684
Bravo
AF:
0.384
Asia WGS
AF:
0.334
AC:
1163
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.061
DANN
Benign
0.29

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: rs2204502; hg19: chr13-85313394; API