11-18709504-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_173588.4(IGSF22):āc.2881A>Gā(p.Thr961Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_173588.4 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGSF22 | NM_173588.4 | c.2881A>G | p.Thr961Ala | missense_variant | 18/23 | ENST00000513874.6 | NP_775859.4 | |
IGSF22 | XM_047426830.1 | c.955A>G | p.Thr319Ala | missense_variant | 5/10 | XP_047282786.1 | ||
IGSF22 | NR_160413.1 | n.2726A>G | non_coding_transcript_exon_variant | 17/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IGSF22 | ENST00000513874.6 | c.2881A>G | p.Thr961Ala | missense_variant | 18/23 | 5 | NM_173588.4 | ENSP00000421191 | P1 | |
IGSF22 | ENST00000504981.5 | n.3221A>G | non_coding_transcript_exon_variant | 17/20 | 1 | |||||
IGSF22-AS1 | ENST00000527285.1 | n.729+2111T>C | intron_variant, non_coding_transcript_variant | 3 | ||||||
IGSF22 | ENST00000319338.6 | c.2578A>G | p.Thr860Ala | missense_variant, NMD_transcript_variant | 17/21 | 2 | ENSP00000322422 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727246
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2022 | The c.2881A>G (p.T961A) alteration is located in exon 18 (coding exon 17) of the IGSF22 gene. This alteration results from a A to G substitution at nucleotide position 2881, causing the threonine (T) at amino acid position 961 to be replaced by an alanine (A). 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
Publications
No publications associated with this variant yet.