rs869320715
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PS1PM2
The NM_001129820.2(SLFN14):c.657A>T(p.Lys219Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,399,372 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin Lovd.
Frequency
Consequence
NM_001129820.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLFN14 | NM_001129820.2 | c.657A>T | p.Lys219Asn | missense_variant | 3/6 | ENST00000674182.1 | |
SLFN14 | XM_017024577.2 | c.657A>T | p.Lys219Asn | missense_variant | 3/6 | ||
SLFN14 | XM_017024578.2 | c.657A>T | p.Lys219Asn | missense_variant | 2/5 | ||
SLFN14 | XM_017024579.2 | c.657A>T | p.Lys219Asn | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLFN14 | ENST00000674182.1 | c.657A>T | p.Lys219Asn | missense_variant | 3/6 | NM_001129820.2 | P1 | ||
SLFN14 | ENST00000415846.3 | c.657A>T | p.Lys219Asn | missense_variant | 1/4 | 1 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1399372Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 690188
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Platelet-type bleeding disorder 20 Pathogenic:1Uncertain:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 02, 2023 | - - |
Uncertain significance, no assertion criteria provided | research | ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology | - | - - |
Thrombocytopenia;C1458140:Abnormal bleeding Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at