rs10447248

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 0.688 in 152,076 control chromosomes in the GnomAD database, including 37,381 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 0.69 ( 37381 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.535
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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:
0.688
AC:
104563
AN:
151956
Hom.:
37326
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.860
Gnomad AMI
AF:
0.746
Gnomad AMR
AF:
0.616
Gnomad ASJ
AF:
0.669
Gnomad EAS
AF:
0.316
Gnomad SAS
AF:
0.398
Gnomad FIN
AF:
0.644
Gnomad MID
AF:
0.639
Gnomad NFE
AF:
0.656
Gnomad OTH
AF:
0.671
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.688
AC:
104669
AN:
152076
Hom.:
37381
Cov.:
31
AF XY:
0.680
AC XY:
50533
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.860
Gnomad4 AMR
AF:
0.615
Gnomad4 ASJ
AF:
0.669
Gnomad4 EAS
AF:
0.315
Gnomad4 SAS
AF:
0.400
Gnomad4 FIN
AF:
0.644
Gnomad4 NFE
AF:
0.656
Gnomad4 OTH
AF:
0.668
Alfa
AF:
0.654
Hom.:
58650
Bravo
AF:
0.694
Asia WGS
AF:
0.420
AC:
1464
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.1
DANN
Benign
0.84

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: rs10447248; hg19: chr5-107915736; COSMIC: COSV60180725; API