rs10511142

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 0.1 in 151,678 control chromosomes in the GnomAD database, including 1,215 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 0.10 ( 1215 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.424
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 (AMR) allele frequency at 95% confidence interval = 0.266 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:
0.100
AC:
15179
AN:
151562
Hom.:
1205
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0242
Gnomad AMI
AF:
0.141
Gnomad AMR
AF:
0.272
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.204
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.0920
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.0972
Gnomad OTH
AF:
0.113
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.100
AC:
15203
AN:
151678
Hom.:
1215
Cov.:
31
AF XY:
0.105
AC XY:
7761
AN XY:
74126
show subpopulations
Gnomad4 AFR
AF:
0.0241
Gnomad4 AMR
AF:
0.273
Gnomad4 ASJ
AF:
0.134
Gnomad4 EAS
AF:
0.203
Gnomad4 SAS
AF:
0.122
Gnomad4 FIN
AF:
0.0920
Gnomad4 NFE
AF:
0.0972
Gnomad4 OTH
AF:
0.112
Alfa
AF:
0.0912
Hom.:
1075
Bravo
AF:
0.116
Asia WGS
AF:
0.173
AC:
600
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.99
DANN
Benign
0.65

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: rs10511142; hg19: chr3-88863054; API