rs10484507

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 0.0796 in 152,266 control chromosomes in the GnomAD database, including 589 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 0.080 ( 589 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.459
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=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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:
0.0796
AC:
12117
AN:
152148
Hom.:
590
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.120
Gnomad AMI
AF:
0.148
Gnomad AMR
AF:
0.0488
Gnomad ASJ
AF:
0.0234
Gnomad EAS
AF:
0.000578
Gnomad SAS
AF:
0.0743
Gnomad FIN
AF:
0.0521
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0754
Gnomad OTH
AF:
0.0664
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0796
AC:
12117
AN:
152266
Hom.:
589
Cov.:
33
AF XY:
0.0768
AC XY:
5721
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.120
Gnomad4 AMR
AF:
0.0487
Gnomad4 ASJ
AF:
0.0234
Gnomad4 EAS
AF:
0.000579
Gnomad4 SAS
AF:
0.0735
Gnomad4 FIN
AF:
0.0521
Gnomad4 NFE
AF:
0.0754
Gnomad4 OTH
AF:
0.0657
Alfa
AF:
0.0732
Hom.:
244
Bravo
AF:
0.0804
Asia WGS
AF:
0.0470
AC:
166
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
1.4
DANN
Benign
0.75

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: rs10484507; hg19: chr6-164606319; API