1-160637394-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003037.5(SLAMF1):c.212A>G(p.Glu71Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000291 in 1,614,108 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003037.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLAMF1 | NM_003037.5 | c.212A>G | p.Glu71Gly | missense_variant | 2/7 | ENST00000302035.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLAMF1 | ENST00000302035.11 | c.212A>G | p.Glu71Gly | missense_variant | 2/7 | 1 | NM_003037.5 | P1 | |
SLAMF1 | ENST00000538290.2 | c.212A>G | p.Glu71Gly | missense_variant | 2/8 | 1 | |||
SLAMF1 | ENST00000494463.1 | n.288A>G | non_coding_transcript_exon_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00135 AC: 205AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000378 AC: 95AN: 251392Hom.: 0 AF XY: 0.000339 AC XY: 46AN XY: 135864
GnomAD4 exome AF: 0.000181 AC: 264AN: 1461794Hom.: 1 Cov.: 31 AF XY: 0.000172 AC XY: 125AN XY: 727200
GnomAD4 genome ? AF: 0.00135 AC: 205AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.00142 AC XY: 106AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at