16-10907064-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000246.4(CIITA):āc.1572C>Gā(p.Ser524=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,455,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. S524S) has been classified as Likely benign.
Frequency
Consequence
NM_000246.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIITA | NM_000246.4 | c.1572C>G | p.Ser524= | synonymous_variant | 11/20 | ENST00000324288.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIITA | ENST00000324288.14 | c.1572C>G | p.Ser524= | synonymous_variant | 11/20 | 1 | NM_000246.4 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000414 AC: 1AN: 241350Hom.: 0 AF XY: 0.00000756 AC XY: 1AN XY: 132210
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1455112Hom.: 0 Cov.: 65 AF XY: 0.00000414 AC XY: 3AN XY: 724138
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
MHC class II deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at