rs4304840
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_080387.5(CLEC4D):āc.94A>Gā(p.Ser32Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 1,467,864 control chromosomes in the GnomAD database, including 45,687 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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_080387.5 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 |
---|---|---|---|---|---|---|---|
CLEC4D | NM_080387.5 | c.94A>G | p.Ser32Gly | missense_variant | 2/6 | ENST00000299665.3 | |
CLEC4D | XM_011520632.3 | c.94A>G | p.Ser32Gly | missense_variant | 3/7 | ||
CLEC4D | XM_047428771.1 | c.94A>G | p.Ser32Gly | missense_variant | 2/6 | ||
CLEC4D | XM_047428772.1 | c.94A>G | p.Ser32Gly | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC4D | ENST00000299665.3 | c.94A>G | p.Ser32Gly | missense_variant | 2/6 | 1 | NM_080387.5 | P1 | |
CLEC4D | ENST00000382064.6 | c.94A>G | p.Ser32Gly | missense_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.315 AC: 47826AN: 151746Hom.: 9414 Cov.: 31
GnomAD3 exomes AF: 0.234 AC: 58438AN: 249968Hom.: 8324 AF XY: 0.233 AC XY: 31450AN XY: 135144
GnomAD4 exome AF: 0.222 AC: 292122AN: 1316000Hom.: 36254 Cov.: 23 AF XY: 0.222 AC XY: 147034AN XY: 662298
GnomAD4 genome ? AF: 0.315 AC: 47903AN: 151864Hom.: 9433 Cov.: 31 AF XY: 0.313 AC XY: 23227AN XY: 74238
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at