rs1026504

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 0.462 in 152,044 control chromosomes in the GnomAD database, including 16,500 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 0.46 ( 16500 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.524
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=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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:
0.462
AC:
70213
AN:
151926
Hom.:
16466
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.474
Gnomad AMI
AF:
0.428
Gnomad AMR
AF:
0.386
Gnomad ASJ
AF:
0.523
Gnomad EAS
AF:
0.432
Gnomad SAS
AF:
0.309
Gnomad FIN
AF:
0.454
Gnomad MID
AF:
0.506
Gnomad NFE
AF:
0.484
Gnomad OTH
AF:
0.440
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.462
AC:
70297
AN:
152044
Hom.:
16500
Cov.:
32
AF XY:
0.458
AC XY:
33999
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.475
Gnomad4 AMR
AF:
0.386
Gnomad4 ASJ
AF:
0.523
Gnomad4 EAS
AF:
0.431
Gnomad4 SAS
AF:
0.309
Gnomad4 FIN
AF:
0.454
Gnomad4 NFE
AF:
0.484
Gnomad4 OTH
AF:
0.443
Alfa
AF:
0.476
Hom.:
34739
Bravo
AF:
0.458
Asia WGS
AF:
0.390
AC:
1357
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.4
DANN
Benign
0.72

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: rs1026504; hg19: chr14-98830005; API