rs10114408

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 0.349 in 151,702 control chromosomes in the GnomAD database, including 9,481 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 0.35 ( 9481 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.15
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=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 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:
0.349
AC:
52924
AN:
151584
Hom.:
9479
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.415
Gnomad AMR
AF:
0.311
Gnomad ASJ
AF:
0.444
Gnomad EAS
AF:
0.205
Gnomad SAS
AF:
0.252
Gnomad FIN
AF:
0.281
Gnomad MID
AF:
0.408
Gnomad NFE
AF:
0.369
Gnomad OTH
AF:
0.382
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.349
AC:
52959
AN:
151702
Hom.:
9481
Cov.:
32
AF XY:
0.342
AC XY:
25348
AN XY:
74138
show subpopulations
Gnomad4 AFR
AF:
0.365
Gnomad4 AMR
AF:
0.311
Gnomad4 ASJ
AF:
0.444
Gnomad4 EAS
AF:
0.205
Gnomad4 SAS
AF:
0.252
Gnomad4 FIN
AF:
0.281
Gnomad4 NFE
AF:
0.369
Gnomad4 OTH
AF:
0.381
Alfa
AF:
0.352
Hom.:
1190
Bravo
AF:
0.353
Asia WGS
AF:
0.292
AC:
1018
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.16
DANN
Benign
0.27

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: rs10114408; hg19: chr9-96631134; API