rs10465428

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 0.422 in 108,561 control chromosomes in the GnomAD database, including 7,691 homozygotes. There are 13,536 hemizygotes in GnomAD. 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 0.42 ( 7691 hom., 13536 hem., cov: 21)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16
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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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:
0.423
AC:
45849
AN:
108506
Hom.:
7693
Cov.:
21
AF XY:
0.437
AC XY:
13512
AN XY:
30924
show subpopulations
Gnomad AFR
AF:
0.268
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.614
Gnomad ASJ
AF:
0.479
Gnomad EAS
AF:
0.997
Gnomad SAS
AF:
0.760
Gnomad FIN
AF:
0.446
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.416
Gnomad OTH
AF:
0.449
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.422
AC:
45866
AN:
108561
Hom.:
7691
Cov.:
21
AF XY:
0.437
AC XY:
13536
AN XY:
30989
show subpopulations
Gnomad4 AFR
AF:
0.268
Gnomad4 AMR
AF:
0.614
Gnomad4 ASJ
AF:
0.479
Gnomad4 EAS
AF:
0.996
Gnomad4 SAS
AF:
0.759
Gnomad4 FIN
AF:
0.446
Gnomad4 NFE
AF:
0.416
Gnomad4 OTH
AF:
0.458
Alfa
AF:
0.249
Hom.:
1171
Bravo
AF:
0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.65
DANN
Benign
0.80

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: rs10465428; hg19: chrX-116699466; API