chr1-27382586-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001330448.1(CD164L2):c.170T>G(p.Leu57Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,396 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001330448.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD164L2 | NM_001330448.1 | c.170T>G | p.Leu57Arg | missense_variant | 2/6 | ENST00000374030.3 | |
CD164L2 | NM_207397.5 | c.170T>G | p.Leu57Arg | missense_variant | 2/5 | ||
CD164L2 | XM_011541441.2 | c.170T>G | p.Leu57Arg | missense_variant | 2/6 | ||
CD164L2 | XR_241190.4 | n.264T>G | non_coding_transcript_exon_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD164L2 | ENST00000374030.3 | c.170T>G | p.Leu57Arg | missense_variant | 2/6 | 5 | NM_001330448.1 | A1 | |
CD164L2 | ENST00000374027.7 | c.170T>G | p.Leu57Arg | missense_variant | 2/5 | 1 | P4 | ||
CD164L2 | ENST00000374025.4 | n.237T>G | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251016Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135744
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461272Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 726954
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2022 | The c.170T>G (p.L57R) alteration is located in exon 2 (coding exon 2) of the CD164L2 gene. This alteration results from a T to G substitution at nucleotide position 170, causing the leucine (L) at amino acid position 57 to be replaced by an arginine (R). 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