chr1-18362168-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_032880.5(IGSF21):c.478C>T(p.Arg160Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R160H) 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGSF21 | NM_032880.5 | c.478C>T | p.Arg160Cys | missense_variant | Exon 5 of 10 | ENST00000251296.4 | NP_116269.3 | |
IGSF21 | XM_017002604.3 | c.460C>T | p.Arg154Cys | missense_variant | Exon 5 of 10 | XP_016858093.1 | ||
IGSF21 | XM_017002605.1 | c.247C>T | p.Arg83Cys | missense_variant | Exon 4 of 9 | XP_016858094.1 | ||
IGSF21 | XM_011542319.4 | c.425-14142C>T | 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.478C>T | p.Arg160Cys | missense_variant | Exon 5 of 10 | 1 | NM_032880.5 | ENSP00000251296.1 | ||
IGSF21 | ENST00000412684.3 | n.335C>T | non_coding_transcript_exon_variant | Exon 4 of 6 | 5 | |||||
IGSF21 | ENST00000497331.2 | n.802C>T | non_coding_transcript_exon_variant | Exon 1 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249664Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134924
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1460964Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726638
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.478C>T (p.R160C) alteration is located in exon 5 (coding exon 5) of the IGSF21 gene. This alteration results from a C to T substitution at nucleotide position 478, causing the arginine (R) at amino acid position 160 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