NM_001555.5:c.3887_3888delCA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PVS1_Moderate
The NM_001555.5(IGSF1):c.3887_3888delCA(p.Thr1296ArgfsTer10) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000331 in 1,208,677 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001555.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000896 AC: 1AN: 111581Hom.: 0 Cov.: 22 AF XY: 0.0000296 AC XY: 1AN XY: 33747
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097096Hom.: 0 AF XY: 0.00000276 AC XY: 1AN XY: 362486
GnomAD4 genome AF: 0.00000896 AC: 1AN: 111581Hom.: 0 Cov.: 22 AF XY: 0.0000296 AC XY: 1AN XY: 33747
ClinVar
Submissions by phenotype
not provided Uncertain:1
The c.3902_3903delCA variant in the IGSF1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.3902_3903delCA variant causes a frameshift starting with codon Threonine 1301, changes this amino acid to an Arginine residue, and creates a premature Stop codon at position 10 of the new reading frame, denoted p.Thr1301ArgfsX10. This variant is predicted to cause loss of normal protein function through protein truncation. The c.3902_3903delCA variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.3902_3903delCA as a likely pathogenic variant. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at