chr1-18365334-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032880.5(IGSF21):c.652C>T(p.Arg218Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,006 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032880.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGSF21 | NM_032880.5 | c.652C>T | p.Arg218Cys | missense_variant | Exon 6 of 10 | ENST00000251296.4 | NP_116269.3 | |
IGSF21 | XM_017002604.3 | c.634C>T | p.Arg212Cys | missense_variant | Exon 6 of 10 | XP_016858093.1 | ||
IGSF21 | XM_017002605.1 | c.421C>T | p.Arg141Cys | missense_variant | Exon 5 of 9 | XP_016858094.1 | ||
IGSF21 | XM_011542319.4 | c.425-10976C>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.652C>T | p.Arg218Cys | missense_variant | Exon 6 of 10 | 1 | NM_032880.5 | ENSP00000251296.1 | ||
IGSF21 | ENST00000412684.3 | n.509C>T | non_coding_transcript_exon_variant | Exon 5 of 6 | 5 | |||||
IGSF21 | ENST00000497331.2 | n.976C>T | non_coding_transcript_exon_variant | Exon 2 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152128Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251274Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135868
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727242
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152128Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.652C>T (p.R218C) alteration is located in exon 6 (coding exon 6) of the IGSF21 gene. This alteration results from a C to T substitution at nucleotide position 652, causing the arginine (R) at amino acid position 218 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