rs10492294

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 0.171 in 152,178 control chromosomes in the GnomAD database, including 2,706 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 0.17 ( 2706 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.576
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 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:
0.171
AC:
25956
AN:
152060
Hom.:
2702
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0492
Gnomad AMI
AF:
0.194
Gnomad AMR
AF:
0.212
Gnomad ASJ
AF:
0.303
Gnomad EAS
AF:
0.151
Gnomad SAS
AF:
0.215
Gnomad FIN
AF:
0.197
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.222
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.171
AC:
25967
AN:
152178
Hom.:
2706
Cov.:
32
AF XY:
0.172
AC XY:
12773
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.0491
Gnomad4 AMR
AF:
0.212
Gnomad4 ASJ
AF:
0.303
Gnomad4 EAS
AF:
0.152
Gnomad4 SAS
AF:
0.215
Gnomad4 FIN
AF:
0.197
Gnomad4 NFE
AF:
0.222
Gnomad4 OTH
AF:
0.186
Alfa
AF:
0.217
Hom.:
8336
Bravo
AF:
0.165
Asia WGS
AF:
0.187
AC:
650
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.1
DANN
Benign
0.65

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: rs10492294; hg19: chr8-129246415; API