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GeneBe

10-50938326-C-G

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 0.467 in 151,606 control chromosomes in the GnomAD database, including 18,401 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 0.47 ( 18401 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750
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=-0.5).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.467
AC:
70759
AN:
151496
Hom.:
18405
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.219
Gnomad AMI
AF:
0.689
Gnomad AMR
AF:
0.502
Gnomad ASJ
AF:
0.517
Gnomad EAS
AF:
0.672
Gnomad SAS
AF:
0.488
Gnomad FIN
AF:
0.582
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.569
Gnomad OTH
AF:
0.486
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.467
AC:
70760
AN:
151606
Hom.:
18401
Cov.:
31
AF XY:
0.470
AC XY:
34807
AN XY:
74036
show subpopulations
Gnomad4 AFR
AF:
0.218
Gnomad4 AMR
AF:
0.502
Gnomad4 ASJ
AF:
0.517
Gnomad4 EAS
AF:
0.672
Gnomad4 SAS
AF:
0.488
Gnomad4 FIN
AF:
0.582
Gnomad4 NFE
AF:
0.569
Gnomad4 OTH
AF:
0.482
Alfa
AF:
0.387
Hom.:
1161
Bravo
AF:
0.454
Asia WGS
AF:
0.560
AC:
1945
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
Cadd
Benign
1.7
Dann
Benign
0.83

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: rs10761612; hg19: chr10-52698086; API