rs10492787

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 0.285 in 152,090 control chromosomes in the GnomAD database, including 6,451 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 0.29 ( 6451 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.420
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 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:
0.285
AC:
43381
AN:
151972
Hom.:
6447
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.212
Gnomad AMI
AF:
0.308
Gnomad AMR
AF:
0.340
Gnomad ASJ
AF:
0.284
Gnomad EAS
AF:
0.406
Gnomad SAS
AF:
0.398
Gnomad FIN
AF:
0.324
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.294
Gnomad OTH
AF:
0.304
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.285
AC:
43409
AN:
152090
Hom.:
6451
Cov.:
33
AF XY:
0.291
AC XY:
21634
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.212
Gnomad4 AMR
AF:
0.340
Gnomad4 ASJ
AF:
0.284
Gnomad4 EAS
AF:
0.406
Gnomad4 SAS
AF:
0.396
Gnomad4 FIN
AF:
0.324
Gnomad4 NFE
AF:
0.294
Gnomad4 OTH
AF:
0.304
Alfa
AF:
0.297
Hom.:
11384
Bravo
AF:
0.281
Asia WGS
AF:
0.429
AC:
1489
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.57
DANN
Benign
0.48

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: rs10492787; hg19: chr16-21226751; API