1-18365262-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032880.5(IGSF21):c.580C>A(p.Pro194Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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. P194S) has been classified as Uncertain significance.
Frequency
Consequence
NM_032880.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGSF21 | NM_032880.5 | c.580C>A | p.Pro194Thr | missense_variant | Exon 6 of 10 | ENST00000251296.4 | NP_116269.3 | |
IGSF21 | XM_017002604.3 | c.562C>A | p.Pro188Thr | missense_variant | Exon 6 of 10 | XP_016858093.1 | ||
IGSF21 | XM_017002605.1 | c.349C>A | p.Pro117Thr | missense_variant | Exon 5 of 9 | XP_016858094.1 | ||
IGSF21 | XM_011542319.4 | c.425-11048C>A | intron_variant | Intron 4 of 7 | XP_011540621.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IGSF21 | ENST00000251296.4 | c.580C>A | p.Pro194Thr | missense_variant | Exon 6 of 10 | 1 | NM_032880.5 | ENSP00000251296.1 | ||
IGSF21 | ENST00000412684.3 | n.437C>A | non_coding_transcript_exon_variant | Exon 5 of 6 | 5 | |||||
IGSF21 | ENST00000497331.2 | n.904C>A | non_coding_transcript_exon_variant | Exon 2 of 6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249446Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134970
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460634Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726506
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.580C>A (p.P194T) alteration is located in exon 6 (coding exon 6) of the IGSF21 gene. This alteration results from a C to A substitution at nucleotide position 580, causing the proline (P) at amino acid position 194 to be replaced by a threonine (T). 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