19-14479438-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005716.4(GIPC1):c.742C>T(p.Arg248Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000612 in 1,421,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R248Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_005716.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GIPC1 | NM_005716.4 | c.742C>T | p.Arg248Trp | missense_variant | 7/9 | ENST00000393033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GIPC1 | ENST00000393033.9 | c.742C>T | p.Arg248Trp | missense_variant | 7/9 | 1 | NM_005716.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000419 AC: 3AN: 71606Hom.: 0 AF XY: 0.0000254 AC XY: 1AN XY: 39416
GnomAD4 exome AF: 0.0000654 AC: 83AN: 1269180Hom.: 0 Cov.: 28 AF XY: 0.0000712 AC XY: 44AN XY: 618362
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2022 | The c.742C>T (p.R248W) alteration is located in exon 7 (coding exon 4) of the GIPC1 gene. This alteration results from a C to T substitution at nucleotide position 742, causing the arginine (R) at amino acid position 248 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at