rs10484429

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 0.101 in 151,998 control chromosomes in the GnomAD database, including 877 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 ( 877 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680
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 (AFR) allele frequency at 95% confidence interval = 0.161 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:
0.101
AC:
15270
AN:
151880
Hom.:
875
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.165
Gnomad AMI
AF:
0.0493
Gnomad AMR
AF:
0.0705
Gnomad ASJ
AF:
0.0462
Gnomad EAS
AF:
0.0850
Gnomad SAS
AF:
0.161
Gnomad FIN
AF:
0.0836
Gnomad MID
AF:
0.123
Gnomad NFE
AF:
0.0709
Gnomad OTH
AF:
0.106
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.101
AC:
15280
AN:
151998
Hom.:
877
Cov.:
32
AF XY:
0.102
AC XY:
7573
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.164
Gnomad4 AMR
AF:
0.0704
Gnomad4 ASJ
AF:
0.0462
Gnomad4 EAS
AF:
0.0850
Gnomad4 SAS
AF:
0.162
Gnomad4 FIN
AF:
0.0836
Gnomad4 NFE
AF:
0.0710
Gnomad4 OTH
AF:
0.105
Alfa
AF:
0.0765
Hom.:
1013
Bravo
AF:
0.102
Asia WGS
AF:
0.110
AC:
382
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
5.9
DANN
Benign
0.45

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: rs10484429; hg19: chr6-48851550; API