X-101356858-G-A
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000061.3(BTK):c.1275C>T(p.Tyr425Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,209,594 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000061.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- Bruton-type agammaglobulinemiaInheritance: XL Classification: DEFINITIVE, SUPPORTIVE Submitted by: Myriad Women’s Health, Orphanet, ClinGen
- isolated growth hormone deficiency type IIIInheritance: XL Classification: STRONG, NO_KNOWN Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
- short stature due to isolated growth hormone deficiency with X-linked hypogammaglobulinemiaInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BTK | NM_000061.3 | c.1275C>T | p.Tyr425Tyr | synonymous_variant | Exon 14 of 19 | ENST00000308731.8 | NP_000052.1 | |
BTK | NM_001287344.2 | c.1377C>T | p.Tyr459Tyr | synonymous_variant | Exon 14 of 19 | NP_001274273.1 | ||
BTK | NM_001287345.2 | c.1038+1516C>T | intron_variant | Intron 13 of 16 | NP_001274274.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000269 AC: 3AN: 111593Hom.: 0 Cov.: 23 show subpopulations
GnomAD2 exomes AF: 0.0000109 AC: 2AN: 183502 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.0000228 AC: 25AN: 1098001Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 5AN XY: 363357 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000269 AC: 3AN: 111593Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1AN XY: 33773 show subpopulations
ClinVar
Submissions by phenotype
X-linked agammaglobulinemia with growth hormone deficiency Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at