3-114120575-A-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 0.533 in 152,098 control chromosomes in the GnomAD database, including 21,720 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 0.53 ( 21720 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.503
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=-0.96).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.595 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:
0.533
AC:
80998
AN:
151978
Hom.:
21709
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.460
Gnomad AMI
AF:
0.520
Gnomad AMR
AF:
0.605
Gnomad ASJ
AF:
0.626
Gnomad EAS
AF:
0.485
Gnomad SAS
AF:
0.544
Gnomad FIN
AF:
0.569
Gnomad MID
AF:
0.671
Gnomad NFE
AF:
0.552
Gnomad OTH
AF:
0.571
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.533
AC:
81040
AN:
152098
Hom.:
21720
Cov.:
33
AF XY:
0.538
AC XY:
40008
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.459
Gnomad4 AMR
AF:
0.605
Gnomad4 ASJ
AF:
0.626
Gnomad4 EAS
AF:
0.486
Gnomad4 SAS
AF:
0.544
Gnomad4 FIN
AF:
0.569
Gnomad4 NFE
AF:
0.552
Gnomad4 OTH
AF:
0.566
Alfa
AF:
0.533
Hom.:
2711
Bravo
AF:
0.533
Asia WGS
AF:
0.498
AC:
1731
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
2.1
DANN
Benign
0.69

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: rs1486012; hg19: chr3-113839422; API