chr1-160565523-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003874.4(CD84):c.269C>T(p.Pro90Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000096 in 1,613,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003874.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD84 | NM_003874.4 | c.269C>T | p.Pro90Leu | missense_variant | 2/7 | ENST00000368054.8 | |
LOC105371468 | XR_922203.3 | n.120-5416G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD84 | ENST00000368054.8 | c.269C>T | p.Pro90Leu | missense_variant | 2/7 | 1 | NM_003874.4 | ||
ENST00000446952.1 | n.116-5416G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251312Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135830
GnomAD4 exome AF: 0.0000937 AC: 137AN: 1461728Hom.: 0 Cov.: 31 AF XY: 0.0000976 AC XY: 71AN XY: 727164
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74406
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.269C>T (p.P90L) alteration is located in exon 2 (coding exon 2) of the CD84 gene. This alteration results from a C to T substitution at nucleotide position 269, causing the proline (P) at amino acid position 90 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