17-35548498-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001129820.2(SLFN14):c.2480G>A(p.Arg827His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000175 in 1,551,730 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001129820.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLFN14 | NM_001129820.2 | c.2480G>A | p.Arg827His | missense_variant | Exon 6 of 6 | ENST00000674182.1 | NP_001123292.1 | |
SLFN14 | XM_017024577.2 | c.2480G>A | p.Arg827His | missense_variant | Exon 6 of 6 | XP_016880066.1 | ||
SLFN14 | XM_017024578.2 | c.2480G>A | p.Arg827His | missense_variant | Exon 5 of 5 | XP_016880067.1 | ||
SLFN14 | XM_017024579.2 | c.2480G>A | p.Arg827His | missense_variant | Exon 5 of 5 | XP_016880068.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLFN14 | ENST00000674182.1 | c.2480G>A | p.Arg827His | missense_variant | Exon 6 of 6 | NM_001129820.2 | ENSP00000501524.1 | |||
SLFN14 | ENST00000415846.3 | c.2480G>A | p.Arg827His | missense_variant | Exon 4 of 4 | 1 | ENSP00000391101.2 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000526 AC: 81AN: 153952Hom.: 1 AF XY: 0.000686 AC XY: 56AN XY: 81688
GnomAD4 exome AF: 0.000184 AC: 257AN: 1399390Hom.: 2 Cov.: 33 AF XY: 0.000255 AC XY: 176AN XY: 690206
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74490
ClinVar
Submissions by phenotype
Platelet-type bleeding disorder 20 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at