8-97277405-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033512.3(TSPYL5):āc.440A>Gā(p.Lys147Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000906 in 1,578,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_033512.3 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 |
---|---|---|---|---|---|---|---|---|
TSPYL5 | NM_033512.3 | c.440A>G | p.Lys147Arg | missense_variant | 1/1 | ENST00000322128.5 | NP_277047.2 | |
LOC101927066 | NR_125390.1 | n.471+141665A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPYL5 | ENST00000322128.5 | c.440A>G | p.Lys147Arg | missense_variant | 1/1 | NM_033512.3 | ENSP00000322802 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000277 AC: 6AN: 216606Hom.: 0 AF XY: 0.0000257 AC XY: 3AN XY: 116782
GnomAD4 exome AF: 0.0000953 AC: 136AN: 1426652Hom.: 0 Cov.: 30 AF XY: 0.0000891 AC XY: 63AN XY: 706984
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2022 | The c.440A>G (p.K147R) alteration is located in exon 1 (coding exon 1) of the TSPYL5 gene. This alteration results from a A to G substitution at nucleotide position 440, causing the lysine (K) at amino acid position 147 to be replaced by an arginine (R). 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