rs1053474
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018439.4(IMPACT):c.*2450G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,916 control chromosomes in the GnomAD database, including 26,186 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 0.57 ( 26186 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
IMPACT
NM_018439.4 3_prime_UTR
NM_018439.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.24
Genes affected
IMPACT (HGNC:20387): (impact RWD domain protein) Predicted to enable actin binding activity and ribosome binding activity. Predicted to be involved in several processes, including GCN2-mediated signaling; cellular response to starvation; and negative regulation of nitrogen compound metabolic process. Predicted to be located in cytoplasm. Predicted to be part of polysome. [provided by Alliance of Genome Resources, Apr 2022]
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=-0.8).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMPACT | NM_018439.4 | c.*2450G>A | 3_prime_UTR_variant | 11/11 | ENST00000284202.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPACT | ENST00000284202.9 | c.*2450G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_018439.4 | P1 | ||
IMPACT | ENST00000581278.1 | c.*43G>A | 3_prime_UTR_variant | 4/4 | 2 | ||||
IMPACT | ENST00000648078.1 | c.*1868G>A | 3_prime_UTR_variant | 12/12 | |||||
IMPACT | ENST00000580035.1 | c.*233G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.568 AC: 86194AN: 151798Hom.: 26182 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
86194
AN:
151798
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.638 AC: 1515AN: 2374Hom.: 483 AF XY: 0.639 AC XY: 694AN XY: 1086
GnomAD3 exomes
AF:
AC:
1515
AN:
2374
Hom.:
AF XY:
AC XY:
694
AN XY:
1086
Gnomad ASJ exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome ? AF: 0.568 AC: 86240AN: 151916Hom.: 26186 Cov.: 32 AF XY: 0.573 AC XY: 42556AN XY: 74248
GnomAD4 genome
?
AF:
AC:
86240
AN:
151916
Hom.:
Cov.:
32
AF XY:
AC XY:
42556
AN XY:
74248
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2194
AN:
3474
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at