chr1-160646913-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003037.5(SLAMF1):c.33C>A(p.Phe11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 1,599,616 control chromosomes in the GnomAD database, including 29,962 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003037.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLAMF1 | NM_003037.5 | c.33C>A | p.Phe11Leu | missense_variant | 1/7 | ENST00000302035.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLAMF1 | ENST00000302035.11 | c.33C>A | p.Phe11Leu | missense_variant | 1/7 | 1 | NM_003037.5 | P1 | |
SLAMF1 | ENST00000538290.2 | c.33C>A | p.Phe11Leu | missense_variant | 1/8 | 1 | |||
SLAMF1 | ENST00000494463.1 | n.109C>A | non_coding_transcript_exon_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.145 AC: 22076AN: 152016Hom.: 2113 Cov.: 32
GnomAD3 exomes AF: 0.169 AC: 41871AN: 248184Hom.: 4180 AF XY: 0.167 AC XY: 22425AN XY: 134086
GnomAD4 exome AF: 0.189 AC: 273000AN: 1447482Hom.: 27847 Cov.: 27 AF XY: 0.187 AC XY: 134482AN XY: 720724
GnomAD4 genome AF: 0.145 AC: 22077AN: 152134Hom.: 2115 Cov.: 32 AF XY: 0.143 AC XY: 10626AN XY: 74372
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at