rs10491859

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 0.128 in 152,162 control chromosomes in the GnomAD database, including 1,363 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 0.13 ( 1363 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.792
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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:
0.128
AC:
19520
AN:
152044
Hom.:
1365
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.176
Gnomad AMI
AF:
0.217
Gnomad AMR
AF:
0.104
Gnomad ASJ
AF:
0.174
Gnomad EAS
AF:
0.0672
Gnomad SAS
AF:
0.0435
Gnomad FIN
AF:
0.104
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.115
Gnomad OTH
AF:
0.134
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.128
AC:
19525
AN:
152162
Hom.:
1363
Cov.:
33
AF XY:
0.126
AC XY:
9373
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.176
Gnomad4 AMR
AF:
0.104
Gnomad4 ASJ
AF:
0.174
Gnomad4 EAS
AF:
0.0674
Gnomad4 SAS
AF:
0.0437
Gnomad4 FIN
AF:
0.104
Gnomad4 NFE
AF:
0.115
Gnomad4 OTH
AF:
0.134
Alfa
AF:
0.121
Hom.:
202
Bravo
AF:
0.132
Asia WGS
AF:
0.0560
AC:
197
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.3
DANN
Benign
0.82

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: rs10491859; hg19: chr9-1510299; API