X-101349783-AG-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_000061.3(BTK):c.*101delC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 699,423 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000061.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BTK | NM_000061.3 | c.*101delC | 3_prime_UTR_variant | Exon 19 of 19 | ENST00000308731.8 | NP_000052.1 | ||
BTK | NM_001287344.2 | c.*101delC | 3_prime_UTR_variant | Exon 19 of 19 | NP_001274273.1 | |||
BTK | NM_001287345.2 | c.*101delC | 3_prime_UTR_variant | Exon 17 of 17 | NP_001274274.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000898 AC: 1AN: 111321Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33519
GnomAD4 exome AF: 0.0000153 AC: 9AN: 588102Hom.: 0 Cov.: 9 AF XY: 0.0000114 AC XY: 2AN XY: 175992
GnomAD4 genome AF: 0.00000898 AC: 1AN: 111321Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33519
ClinVar
Submissions by phenotype
not provided Uncertain:1
Variant summary: The c.*101delC in BTK gene is a deletion of conserved nucleotide in 3' UTR region. Mutation Taster algorithm predicts this change to not affect a poly(A) signal, however, no stability studies were published at the time of evaluation. The presence of the variant in the general population could not be determined at this time as this region is not covered the control population dataset of ExAC and has not, to our knowledge, been reported in affected individuals via published reports or by reputable databases/clinical laboratories. An internal subject (famale) carrying this variant also carried c.799_806delAACTATGTT (evaluated as likely pathogenic); however, phase of the variants are unknown. Taken together, the variant was classified as VUS. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at