ENST00000441026.1:n.103+7090C>T

Variant summary

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

The ENST00000441026.1(ENSG00000234172):​n.103+7090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 151,964 control chromosomes in the GnomAD database, including 50,477 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 0.81 ( 50477 hom., cov: 33)

Consequence

ENSG00000234172
ENST00000441026.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.587
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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 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
ENSG00000234172ENST00000441026.1 linkn.103+7090C>T intron_variant Intron 1 of 2 2

Frequencies

GnomAD3 genomes
AF:
0.812
AC:
123271
AN:
151846
Hom.:
50452
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.723
Gnomad AMI
AF:
0.939
Gnomad AMR
AF:
0.871
Gnomad ASJ
AF:
0.803
Gnomad EAS
AF:
0.881
Gnomad SAS
AF:
0.840
Gnomad FIN
AF:
0.736
Gnomad MID
AF:
0.736
Gnomad NFE
AF:
0.856
Gnomad OTH
AF:
0.819
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.812
AC:
123348
AN:
151964
Hom.:
50477
Cov.:
33
AF XY:
0.809
AC XY:
60119
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.723
Gnomad4 AMR
AF:
0.871
Gnomad4 ASJ
AF:
0.803
Gnomad4 EAS
AF:
0.881
Gnomad4 SAS
AF:
0.841
Gnomad4 FIN
AF:
0.736
Gnomad4 NFE
AF:
0.856
Gnomad4 OTH
AF:
0.818
Alfa
AF:
0.837
Hom.:
6654
Bravo
AF:
0.817
Asia WGS
AF:
0.837
AC:
2896
AN:
3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
3.9
DANN
Benign
0.13

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: rs826133; hg19: chr2-184776448; API