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GeneBe

rs10495285

Positions:

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 0.254 in 152,182 control chromosomes in the GnomAD database, including 5,852 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 0.25 ( 5852 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.379
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.254
AC:
38577
AN:
152064
Hom.:
5849
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0980
Gnomad AMI
AF:
0.270
Gnomad AMR
AF:
0.263
Gnomad ASJ
AF:
0.369
Gnomad EAS
AF:
0.0714
Gnomad SAS
AF:
0.302
Gnomad FIN
AF:
0.322
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.339
Gnomad OTH
AF:
0.268
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.254
AC:
38580
AN:
152182
Hom.:
5852
Cov.:
33
AF XY:
0.250
AC XY:
18619
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.0978
Gnomad4 AMR
AF:
0.263
Gnomad4 ASJ
AF:
0.369
Gnomad4 EAS
AF:
0.0710
Gnomad4 SAS
AF:
0.303
Gnomad4 FIN
AF:
0.322
Gnomad4 NFE
AF:
0.339
Gnomad4 OTH
AF:
0.268
Alfa
AF:
0.194
Hom.:
519
Bravo
AF:
0.242
Asia WGS
AF:
0.184
AC:
642
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.38
DANN
Benign
0.35

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: rs10495285; hg19: chr1-229804995; API