21-33432706-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005534.4(IFNGR2):c.722-8C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005534.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNGR2 | NM_005534.4 | c.722-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000290219.11 | |||
TMEM50B | XM_011529746.3 | c.*2327G>C | 3_prime_UTR_variant | 10/10 | |||
IFNGR2 | NM_001329128.2 | c.779-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
TMEM50B | NR_040016.2 | n.2872G>C | non_coding_transcript_exon_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNGR2 | ENST00000290219.11 | c.722-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005534.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152114Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251340Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135844
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461822Hom.: 0 Cov.: 35 AF XY: 0.0000371 AC XY: 27AN XY: 727216
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152114Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
Immunodeficiency 28 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at