17-7076150-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182906.4(CLEC10A):c.355G>T(p.Val119Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182906.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152018Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249096Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134718
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461572Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 727096
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152018Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.355G>T (p.V119L) alteration is located in exon 6 (coding exon 5) of the CLEC10A gene. This alteration results from a G to T substitution at nucleotide position 355, causing the valine (V) at amino acid position 119 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at