rs3024505

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 0.112 in 152,218 control chromosomes in the GnomAD database, including 1,196 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 0.11 ( 1196 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.244
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=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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:
0.113
AC:
17116
AN:
152098
Hom.:
1196
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0461
Gnomad AMI
AF:
0.112
Gnomad AMR
AF:
0.0816
Gnomad ASJ
AF:
0.135
Gnomad EAS
AF:
0.0254
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.167
Gnomad MID
AF:
0.137
Gnomad NFE
AF:
0.157
Gnomad OTH
AF:
0.123
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.112
AC:
17110
AN:
152218
Hom.:
1196
Cov.:
33
AF XY:
0.111
AC XY:
8243
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.0461
Gnomad4 AMR
AF:
0.0814
Gnomad4 ASJ
AF:
0.135
Gnomad4 EAS
AF:
0.0251
Gnomad4 SAS
AF:
0.109
Gnomad4 FIN
AF:
0.167
Gnomad4 NFE
AF:
0.157
Gnomad4 OTH
AF:
0.122
Alfa
AF:
0.144
Hom.:
3275
Bravo
AF:
0.103
Asia WGS
AF:
0.0570
AC:
198
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
2.8
DANN
Benign
0.59

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: rs3024505; hg19: chr1-206939904; API