chr6-137215318-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001363526.1(IFNGR1):c.4C>T(p.Leu2Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,545,614 control chromosomes in the GnomAD database, including 17,597 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001363526.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFNGR1 | NM_000416.3 | c.85+3925C>T | intron_variant | Intron 1 of 6 | ENST00000367739.9 | NP_000407.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.122 AC: 18582AN: 152046Hom.: 1294 Cov.: 32
GnomAD3 exomes AF: 0.128 AC: 18943AN: 147932Hom.: 1391 AF XY: 0.128 AC XY: 10206AN XY: 79680
GnomAD4 exome AF: 0.149 AC: 206939AN: 1393450Hom.: 16300 Cov.: 31 AF XY: 0.148 AC XY: 101391AN XY: 687266
GnomAD4 genome AF: 0.122 AC: 18581AN: 152164Hom.: 1297 Cov.: 32 AF XY: 0.119 AC XY: 8842AN XY: 74390
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 23% of patients studied by a panel of primary immunodeficiencies. Number of patients: 20. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at