chr1-185301455-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_006469.5(IVNS1ABP):c.874G>A(p.Val292Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,050 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
Frequency
Consequence
NM_006469.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IVNS1ABP | NM_006469.5 | c.874G>A | p.Val292Ile | missense_variant | 9/15 | ENST00000367498.8 | |
IVNS1ABP | XM_047434070.1 | c.874G>A | p.Val292Ile | missense_variant | 9/15 | ||
IVNS1ABP | XM_047434096.1 | c.607G>A | p.Val203Ile | missense_variant | 8/14 | ||
IVNS1ABP | XM_047434109.1 | c.220G>A | p.Val74Ile | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IVNS1ABP | ENST00000367498.8 | c.874G>A | p.Val292Ile | missense_variant | 9/15 | 1 | NM_006469.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251002Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135654
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460922Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726746
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74320
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | IVNS1ABP: BP4, BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at