chr4-68228834-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182502.3(TMPRSS11B):āc.997A>Gā(p.Lys333Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000123 in 1,461,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_182502.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMPRSS11B | NM_182502.3 | c.997A>G | p.Lys333Glu | missense_variant | 9/10 | ENST00000332644.6 | NP_872308.2 | |
TMPRSS11B | XM_011531608.3 | c.997A>G | p.Lys333Glu | missense_variant | 9/11 | XP_011529910.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMPRSS11B | ENST00000332644.6 | c.997A>G | p.Lys333Glu | missense_variant | 9/10 | 1 | NM_182502.3 | ENSP00000330475.5 | ||
TMPRSS11B | ENST00000510856.1 | n.473A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250568Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135388
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461568Hom.: 0 Cov.: 40 AF XY: 0.0000165 AC XY: 12AN XY: 727068
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 01, 2023 | The c.997A>G (p.K333E) alteration is located in exon 9 (coding exon 9) of the TMPRSS11B gene. This alteration results from a A to G substitution at nucleotide position 997, causing the lysine (K) at amino acid position 333 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at