21-33432772-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_005534.4(IFNGR2):c.780G>A(p.Ser260=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,614,030 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S260S) has been classified as Uncertain significance.
Frequency
Consequence
NM_005534.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNGR2 | NM_005534.4 | c.780G>A | p.Ser260= | synonymous_variant | 6/7 | ENST00000290219.11 | |
IFNGR2 | NM_001329128.2 | c.837G>A | p.Ser279= | synonymous_variant | 7/8 | ||
TMEM50B | XM_011529746.3 | c.*2261C>T | 3_prime_UTR_variant | 10/10 | |||
TMEM50B | NR_040016.2 | n.2806C>T | non_coding_transcript_exon_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNGR2 | ENST00000290219.11 | c.780G>A | p.Ser260= | synonymous_variant | 6/7 | 1 | NM_005534.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152088Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251322Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135822
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461824Hom.: 1 Cov.: 34 AF XY: 0.0000715 AC XY: 52AN XY: 727230
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152206Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74410
ClinVar
Submissions by phenotype
Immunodeficiency 28 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at