5-148107110-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006846.4(SPINK5):c.1553G>T(p.Arg518Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R518C) has been classified as Benign.
Frequency
Consequence
NM_006846.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPINK5 | NM_006846.4 | c.1553G>T | p.Arg518Leu | missense_variant | 17/33 | ENST00000256084.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPINK5 | ENST00000256084.8 | c.1553G>T | p.Arg518Leu | missense_variant | 17/33 | 1 | NM_006846.4 | P2 | |
FBXO38-DT | ENST00000667608.1 | n.1257-13368C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249518Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135374
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461090Hom.: 0 Cov.: 29 AF XY: 0.00000688 AC XY: 5AN XY: 726890
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at