1-27383169-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001330448.1(CD164L2):c.71C>T(p.Ala24Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,548,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD164L2 | NM_001330448.1 | c.71C>T | p.Ala24Val | missense_variant | 1/6 | ENST00000374030.3 | |
CD164L2 | NM_207397.5 | c.71C>T | p.Ala24Val | missense_variant | 1/5 | ||
CD164L2 | XM_011541441.2 | c.71C>T | p.Ala24Val | missense_variant | 1/6 | ||
CD164L2 | XR_241190.4 | n.165C>T | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD164L2 | ENST00000374030.3 | c.71C>T | p.Ala24Val | missense_variant | 1/6 | 5 | NM_001330448.1 | A1 | |
CD164L2 | ENST00000374027.7 | c.71C>T | p.Ala24Val | missense_variant | 1/5 | 1 | P4 | ||
CD164L2 | ENST00000374025.4 | n.138C>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152258Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000338 AC: 5AN: 147758Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 78954
GnomAD4 exome AF: 0.0000150 AC: 21AN: 1396174Hom.: 0 Cov.: 31 AF XY: 0.0000102 AC XY: 7AN XY: 688662
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152258Hom.: 0 Cov.: 31 AF XY: 0.000134 AC XY: 10AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.71C>T (p.A24V) alteration is located in exon 1 (coding exon 1) of the CD164L2 gene. This alteration results from a C to T substitution at nucleotide position 71, causing the alanine (A) at amino acid position 24 to be replaced by a valine (V). 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