rs12292796

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 0.101 in 152,170 control chromosomes in the GnomAD database, including 1,088 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 0.10 ( 1088 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.41
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=-1.04).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.101
AC:
15300
AN:
152050
Hom.:
1084
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.198
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0481
Gnomad ASJ
AF:
0.139
Gnomad EAS
AF:
0.0582
Gnomad SAS
AF:
0.161
Gnomad FIN
AF:
0.0507
Gnomad MID
AF:
0.117
Gnomad NFE
AF:
0.0592
Gnomad OTH
AF:
0.0936
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.101
AC:
15315
AN:
152170
Hom.:
1088
Cov.:
32
AF XY:
0.0999
AC XY:
7433
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.198
Gnomad4 AMR
AF:
0.0480
Gnomad4 ASJ
AF:
0.139
Gnomad4 EAS
AF:
0.0583
Gnomad4 SAS
AF:
0.161
Gnomad4 FIN
AF:
0.0507
Gnomad4 NFE
AF:
0.0592
Gnomad4 OTH
AF:
0.0935
Alfa
AF:
0.0797
Hom.:
131
Bravo
AF:
0.102
Asia WGS
AF:
0.102
AC:
354
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.092
DANN
Benign
0.46

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: rs12292796; hg19: chr11-39426099; API