12-10118534-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_197947.3(CLEC7A):āc.668T>Gā(p.Ile223Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00187 in 1,612,906 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_197947.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC7A | NM_197947.3 | c.668T>G | p.Ile223Ser | missense_variant | 6/6 | ENST00000304084.13 | |
LOC105369655 | XR_007063208.1 | n.181+2991A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC7A | ENST00000304084.13 | c.668T>G | p.Ile223Ser | missense_variant | 6/6 | 1 | NM_197947.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0102 AC: 1558AN: 152220Hom.: 27 Cov.: 32
GnomAD3 exomes AF: 0.00249 AC: 626AN: 251372Hom.: 9 AF XY: 0.00173 AC XY: 235AN XY: 135862
GnomAD4 exome AF: 0.000998 AC: 1458AN: 1460568Hom.: 19 Cov.: 31 AF XY: 0.000925 AC XY: 672AN XY: 726704
GnomAD4 genome AF: 0.0102 AC: 1560AN: 152338Hom.: 27 Cov.: 32 AF XY: 0.00964 AC XY: 718AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 28, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at