rs150681845
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_015693.4(INTU):c.1354G>A(p.Ala452Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00239 in 1,613,458 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_015693.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INTU | NM_015693.4 | c.1354G>A | p.Ala452Thr | missense_variant | 8/16 | ENST00000335251.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTU | ENST00000335251.11 | c.1354G>A | p.Ala452Thr | missense_variant | 8/16 | 1 | NM_015693.4 | P1 | |
INTU | ENST00000503952.5 | c.*111G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/17 | 1 | ||||
INTU | ENST00000503626.5 | c.*2621G>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/18 | 2 | ||||
INTU | ENST00000506283.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00189 AC: 287AN: 152066Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00263 AC: 660AN: 250842Hom.: 3 AF XY: 0.00301 AC XY: 408AN XY: 135544
GnomAD4 exome AF: 0.00245 AC: 3578AN: 1461274Hom.: 17 Cov.: 30 AF XY: 0.00266 AC XY: 1932AN XY: 726942
GnomAD4 genome ? AF: 0.00188 AC: 286AN: 152184Hom.: 2 Cov.: 32 AF XY: 0.00196 AC XY: 146AN XY: 74426
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Uncertain significance, no assertion criteria provided | literature only | OMIM | Apr 02, 2018 | - - |
Growth delay;C0687120:Nephronophthisis Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | May 09, 2016 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
INTU-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 01, 2022 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at