rs10484702

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 0.474 in 151,948 control chromosomes in the GnomAD database, including 18,095 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 ( 18095 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.53
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=-0.82).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.62 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:
0.474
AC:
71972
AN:
151830
Hom.:
18092
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.305
Gnomad AMI
AF:
0.662
Gnomad AMR
AF:
0.630
Gnomad ASJ
AF:
0.595
Gnomad EAS
AF:
0.630
Gnomad SAS
AF:
0.613
Gnomad FIN
AF:
0.438
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.515
Gnomad OTH
AF:
0.527
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.474
AC:
71996
AN:
151948
Hom.:
18095
Cov.:
32
AF XY:
0.478
AC XY:
35469
AN XY:
74248
show subpopulations
Gnomad4 AFR
AF:
0.305
Gnomad4 AMR
AF:
0.631
Gnomad4 ASJ
AF:
0.595
Gnomad4 EAS
AF:
0.630
Gnomad4 SAS
AF:
0.613
Gnomad4 FIN
AF:
0.438
Gnomad4 NFE
AF:
0.515
Gnomad4 OTH
AF:
0.527
Alfa
AF:
0.523
Hom.:
43000
Bravo
AF:
0.482
Asia WGS
AF:
0.546
AC:
1896
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
9.8
DANN
Benign
0.58

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: rs10484702; hg19: chr6-145528057; API