21-33432772-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1
The NM_005534.4(IFNGR2):c.780G>A(p.Ser260Ser) 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 Conflicting classifications of pathogenicity (no stars). 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 -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFNGR2 | NM_005534.4 | c.780G>A | p.Ser260Ser | synonymous_variant | Exon 6 of 7 | ENST00000290219.11 | NP_005525.2 | |
IFNGR2 | NM_001329128.2 | c.837G>A | p.Ser279Ser | synonymous_variant | Exon 7 of 8 | NP_001316057.1 | ||
TMEM50B | XM_011529746.3 | c.*2261C>T | 3_prime_UTR_variant | Exon 10 of 10 | XP_011528048.1 | |||
TMEM50B | NR_040016.2 | n.2806C>T | non_coding_transcript_exon_variant | Exon 9 of 9 |
Ensembl
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 Uncertain:1Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at