rs10127175
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001569.4(IRAK1):c.607T>A(p.Cys203Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00351 in 1,087,651 control chromosomes in the GnomAD database, including 106 homozygotes. There are 925 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001569.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRAK1 | NM_001569.4 | c.607T>A | p.Cys203Ser | missense_variant | 5/14 | ENST00000369980.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRAK1 | ENST00000369980.8 | c.607T>A | p.Cys203Ser | missense_variant | 5/14 | 1 | NM_001569.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0174 AC: 1915AN: 109841Hom.: 50 Cov.: 22 AF XY: 0.0144 AC XY: 464AN XY: 32143
GnomAD3 exomes AF: 0.00507 AC: 923AN: 182162Hom.: 21 AF XY: 0.00310 AC XY: 208AN XY: 67010
GnomAD4 exome AF: 0.00194 AC: 1899AN: 977759Hom.: 56 Cov.: 23 AF XY: 0.00167 AC XY: 459AN XY: 275549
GnomAD4 genome ? AF: 0.0175 AC: 1921AN: 109892Hom.: 50 Cov.: 22 AF XY: 0.0145 AC XY: 466AN XY: 32204
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at