7-141943898-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013252.3(CLEC5A):c.206C>A(p.Thr69Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000624 in 1,602,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013252.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC5A | NM_013252.3 | c.206C>A | p.Thr69Lys | missense_variant, splice_region_variant | 4/7 | ENST00000546910.6 | |
CLEC5A | NM_001301167.2 | c.139+1443C>A | intron_variant | ||||
CLEC5A | XM_011515995.3 | c.79+2316C>A | intron_variant | ||||
CLEC5A | XR_007059995.1 | n.394C>A | splice_region_variant, non_coding_transcript_exon_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC5A | ENST00000546910.6 | c.206C>A | p.Thr69Lys | missense_variant, splice_region_variant | 4/7 | 1 | NM_013252.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251266Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135800
GnomAD4 exome AF: 0.00000552 AC: 8AN: 1450572Hom.: 0 Cov.: 27 AF XY: 0.00000138 AC XY: 1AN XY: 722260
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | The c.206C>A (p.T69K) alteration is located in exon 4 (coding exon 3) of the CLEC5A gene. This alteration results from a C to A substitution at nucleotide position 206, causing the threonine (T) at amino acid position 69 to be replaced by a lysine (K). 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