rs10879490

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 0.299 in 152,094 control chromosomes in the GnomAD database, including 9,213 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 0.30 ( 9213 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39
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=-0.67).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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:
0.300
AC:
45552
AN:
151976
Hom.:
9216
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0739
Gnomad AMI
AF:
0.343
Gnomad AMR
AF:
0.256
Gnomad ASJ
AF:
0.350
Gnomad EAS
AF:
0.00346
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.521
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.436
Gnomad OTH
AF:
0.304
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.299
AC:
45540
AN:
152094
Hom.:
9213
Cov.:
32
AF XY:
0.302
AC XY:
22464
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.0737
Gnomad4 AMR
AF:
0.256
Gnomad4 ASJ
AF:
0.350
Gnomad4 EAS
AF:
0.00347
Gnomad4 SAS
AF:
0.236
Gnomad4 FIN
AF:
0.521
Gnomad4 NFE
AF:
0.436
Gnomad4 OTH
AF:
0.300
Alfa
AF:
0.364
Hom.:
1514
Bravo
AF:
0.268
Asia WGS
AF:
0.110
AC:
381
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
14
DANN
Benign
0.78

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: rs10879490; hg19: chr12-73163151; API