rs10485285

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 0.375 in 151,812 control chromosomes in the GnomAD database, including 10,999 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 0.37 ( 10999 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0270
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=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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:
0.375
AC:
56817
AN:
151694
Hom.:
10974
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.426
Gnomad AMI
AF:
0.332
Gnomad AMR
AF:
0.251
Gnomad ASJ
AF:
0.339
Gnomad EAS
AF:
0.481
Gnomad SAS
AF:
0.521
Gnomad FIN
AF:
0.413
Gnomad MID
AF:
0.275
Gnomad NFE
AF:
0.350
Gnomad OTH
AF:
0.337
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.375
AC:
56901
AN:
151812
Hom.:
10999
Cov.:
31
AF XY:
0.380
AC XY:
28169
AN XY:
74182
show subpopulations
Gnomad4 AFR
AF:
0.427
Gnomad4 AMR
AF:
0.252
Gnomad4 ASJ
AF:
0.339
Gnomad4 EAS
AF:
0.481
Gnomad4 SAS
AF:
0.520
Gnomad4 FIN
AF:
0.413
Gnomad4 NFE
AF:
0.350
Gnomad4 OTH
AF:
0.341
Alfa
AF:
0.352
Hom.:
15527
Bravo
AF:
0.357
Asia WGS
AF:
0.499
AC:
1735
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
2.3
DANN
Benign
0.50

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: rs10485285; hg19: chr6-81478607; API