GeneBe

ENST00000645383.1:n.393+1339_393+1340insG

Variant names:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000645383.1(ENSG00000285163):​n.393+1339_393+1340insG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.72 ( 38608 hom., cov: 0)

Consequence

ENSG00000285163
ENST00000645383.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.902
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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
ENSG00000285163ENST00000645383.1 linkn.393+1339_393+1340insG intron_variant Intron 1 of 3
ENSG00000285163ENST00000646214.1 linkn.77+8553_77+8554insG intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.719
AC:
104792
AN:
145810
Hom.:
38557
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.895
Gnomad AMI
AF:
0.680
Gnomad AMR
AF:
0.703
Gnomad ASJ
AF:
0.567
Gnomad EAS
AF:
0.760
Gnomad SAS
AF:
0.667
Gnomad FIN
AF:
0.724
Gnomad MID
AF:
0.517
Gnomad NFE
AF:
0.629
Gnomad OTH
AF:
0.657
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.719
AC:
104890
AN:
145890
Hom.:
38608
Cov.:
0
AF XY:
0.721
AC XY:
50754
AN XY:
70346
show subpopulations
Gnomad4 AFR
AF:
0.895
Gnomad4 AMR
AF:
0.704
Gnomad4 ASJ
AF:
0.567
Gnomad4 EAS
AF:
0.761
Gnomad4 SAS
AF:
0.667
Gnomad4 FIN
AF:
0.724
Gnomad4 NFE
AF:
0.629
Gnomad4 OTH
AF:
0.659
Alfa
AF:
0.482
Hom.:
1077
Asia WGS
AF:
0.721
AC:
2496
AN:
3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs11398689; hg19: chr16-85967219; API