21-39771170-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080444.2(IGSF5):c.673C>T(p.Arg225Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,599,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080444.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGSF5 | NM_001080444.2 | c.673C>T | p.Arg225Cys | missense_variant | 4/9 | ENST00000380588.5 | |
IGSF5 | XM_047440699.1 | c.943C>T | p.Arg315Cys | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGSF5 | ENST00000380588.5 | c.673C>T | p.Arg225Cys | missense_variant | 4/9 | 1 | NM_001080444.2 | P1 | |
IGSF5 | ENST00000479378.1 | n.779C>T | non_coding_transcript_exon_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000860 AC: 21AN: 244264Hom.: 0 AF XY: 0.0000834 AC XY: 11AN XY: 131938
GnomAD4 exome AF: 0.000117 AC: 169AN: 1447048Hom.: 0 Cov.: 32 AF XY: 0.000116 AC XY: 83AN XY: 718088
GnomAD4 genome AF: 0.000118 AC: 18AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 01, 2024 | The c.673C>T (p.R225C) alteration is located in exon 4 (coding exon 4) of the IGSF5 gene. This alteration results from a C to T substitution at nucleotide position 673, causing the arginine (R) at amino acid position 225 to be replaced by a cysteine (C). 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