chr3-118395843-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000482142.5(ENSG00000243276):​n.232+100780G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,134 control chromosomes in the GnomAD database, including 44,481 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 0.76 ( 44481 hom., cov: 33)

Consequence

ENSG00000243276
ENST00000482142.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.489
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 = 0.896 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
ENSG00000243276ENST00000482142.5 linkn.232+100780G>A intron_variant Intron 3 of 6 5

Frequencies

GnomAD3 genomes
AF:
0.759
AC:
115342
AN:
152016
Hom.:
44437
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.903
Gnomad AMI
AF:
0.596
Gnomad AMR
AF:
0.728
Gnomad ASJ
AF:
0.718
Gnomad EAS
AF:
0.815
Gnomad SAS
AF:
0.663
Gnomad FIN
AF:
0.648
Gnomad MID
AF:
0.737
Gnomad NFE
AF:
0.702
Gnomad OTH
AF:
0.742
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.759
AC:
115442
AN:
152134
Hom.:
44481
Cov.:
33
AF XY:
0.757
AC XY:
56295
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.903
Gnomad4 AMR
AF:
0.728
Gnomad4 ASJ
AF:
0.718
Gnomad4 EAS
AF:
0.815
Gnomad4 SAS
AF:
0.662
Gnomad4 FIN
AF:
0.648
Gnomad4 NFE
AF:
0.702
Gnomad4 OTH
AF:
0.739
Alfa
AF:
0.714
Hom.:
21248
Bravo
AF:
0.772
Asia WGS
AF:
0.714
AC:
2486
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
1.1
DANN
Benign
0.60

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: rs500097; hg19: chr3-118114690; API