chr4-127633138-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015693.4(INTU):āc.104T>Cā(p.Val35Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00161 in 1,614,036 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_015693.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INTU | NM_015693.4 | c.104T>C | p.Val35Ala | missense_variant | 1/16 | ENST00000335251.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTU | ENST00000335251.11 | c.104T>C | p.Val35Ala | missense_variant | 1/16 | 1 | NM_015693.4 | P1 | |
INTU | ENST00000503952.5 | c.104T>C | p.Val35Ala | missense_variant, NMD_transcript_variant | 1/17 | 1 | |||
INTU | ENST00000504491.1 | c.89+9647T>C | intron_variant | 4 | |||||
INTU | ENST00000503626.5 | c.104T>C | p.Val35Ala | missense_variant, NMD_transcript_variant | 1/18 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00245 AC: 373AN: 152196Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00373 AC: 939AN: 251422Hom.: 13 AF XY: 0.00321 AC XY: 436AN XY: 135888
GnomAD4 exome AF: 0.00152 AC: 2222AN: 1461722Hom.: 47 Cov.: 31 AF XY: 0.00144 AC XY: 1048AN XY: 727152
GnomAD4 genome AF: 0.00249 AC: 380AN: 152314Hom.: 5 Cov.: 32 AF XY: 0.00289 AC XY: 215AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | - - |
INTU-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 23, 2019 | 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