chr12-10118463-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_197947.3(CLEC7A):c.739A>T(p.Met247Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 1,609,242 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. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_197947.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC7A | NM_197947.3 | c.739A>T | p.Met247Leu | missense_variant | 6/6 | ENST00000304084.13 | |
LOC105369655 | XR_007063208.1 | n.181+2920T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC7A | ENST00000304084.13 | c.739A>T | p.Met247Leu | missense_variant | 6/6 | 1 | NM_197947.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000933 AC: 142AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000227 AC: 57AN: 250682Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135544
GnomAD4 exome AF: 0.0000728 AC: 106AN: 1456902Hom.: 0 Cov.: 31 AF XY: 0.0000607 AC XY: 44AN XY: 725048
GnomAD4 genome ? AF: 0.000939 AC: 143AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.000832 AC XY: 62AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2018 | - - |
CLEC7A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 22, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at