11-18709437-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173588.4(IGSF22):c.2948T>A(p.Val983Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173588.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGSF22 | NM_173588.4 | c.2948T>A | p.Val983Asp | missense_variant | 18/23 | ENST00000513874.6 | NP_775859.4 | |
IGSF22 | XM_047426830.1 | c.1022T>A | p.Val341Asp | missense_variant | 5/10 | XP_047282786.1 | ||
IGSF22 | NR_160413.1 | n.2793T>A | non_coding_transcript_exon_variant | 17/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IGSF22 | ENST00000513874.6 | c.2948T>A | p.Val983Asp | missense_variant | 18/23 | 5 | NM_173588.4 | ENSP00000421191 | P1 | |
IGSF22 | ENST00000504981.5 | n.3288T>A | non_coding_transcript_exon_variant | 17/20 | 1 | |||||
IGSF22-AS1 | ENST00000527285.1 | n.729+2044A>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
IGSF22 | ENST00000319338.6 | c.2645T>A | p.Val882Asp | missense_variant, NMD_transcript_variant | 17/21 | 2 | ENSP00000322422 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151698Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249554Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135400
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461880Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727238
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151698Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74068
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | The c.2948T>A (p.V983D) alteration is located in exon 18 (coding exon 17) of the IGSF22 gene. This alteration results from a T to A substitution at nucleotide position 2948, causing the valine (V) at amino acid position 983 to be replaced by an aspartic acid (D). 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