12-27806972-C-T

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 0.098 in 151,814 control chromosomes in the GnomAD database, including 927 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 0.098 ( 927 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.696
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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 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:
0.0981
AC:
14880
AN:
151720
Hom.:
928
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0347
Gnomad AMI
AF:
0.0439
Gnomad AMR
AF:
0.0924
Gnomad ASJ
AF:
0.164
Gnomad EAS
AF:
0.00212
Gnomad SAS
AF:
0.126
Gnomad FIN
AF:
0.0652
Gnomad MID
AF:
0.201
Gnomad NFE
AF:
0.145
Gnomad OTH
AF:
0.101
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0980
AC:
14874
AN:
151814
Hom.:
927
Cov.:
31
AF XY:
0.0957
AC XY:
7096
AN XY:
74146
show subpopulations
Gnomad4 AFR
AF:
0.0347
Gnomad4 AMR
AF:
0.0921
Gnomad4 ASJ
AF:
0.164
Gnomad4 EAS
AF:
0.00213
Gnomad4 SAS
AF:
0.126
Gnomad4 FIN
AF:
0.0652
Gnomad4 NFE
AF:
0.145
Gnomad4 OTH
AF:
0.0997
Alfa
AF:
0.133
Hom.:
676
Bravo
AF:
0.0962

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.7
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: rs7311374; hg19: chr12-27959905; API