rs142749099
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 6P and 8B. PVS1_StrongPM2BP6_Very_Strong
The NM_001411144.1(GIPC3):c.928C>T(p.Arg310*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000591 in 1,606,118 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 Likely benign (★★).
Frequency
Consequence
NM_001411144.1 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GIPC3 | ENST00000644452.3 | c.915C>T | p.Gly305Gly | synonymous_variant | Exon 6 of 6 | NM_133261.3 | ENSP00000493901.2 | |||
GIPC3 | ENST00000644946.1 | c.928C>T | p.Arg310* | stop_gained | Exon 6 of 6 | ENSP00000495068.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000429 AC: 10AN: 233246Hom.: 0 AF XY: 0.0000474 AC XY: 6AN XY: 126630
GnomAD4 exome AF: 0.0000619 AC: 90AN: 1453948Hom.: 0 Cov.: 35 AF XY: 0.0000609 AC XY: 44AN XY: 722460
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:1
p.Gly305Gly in Exon 06 of GIPC3: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 7/39346 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitu te.org; dbSNP rs142749099). -
Autosomal recessive nonsyndromic hearing loss 15 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at