chr11-61009722-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006725.5(CD6):c.932C>A(p.Ala311Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006725.5 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 |
---|---|---|---|---|---|---|---|
CD6 | NM_006725.5 | c.932C>A | p.Ala311Glu | missense_variant | 5/13 | ENST00000313421.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD6 | ENST00000313421.11 | c.932C>A | p.Ala311Glu | missense_variant | 5/13 | 1 | NM_006725.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000644 AC: 98AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000139 AC: 35AN: 251214Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135818
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461752Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 30AN XY: 727176
GnomAD4 genome ? AF: 0.000644 AC: 98AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.932C>A (p.A311E) alteration is located in exon 5 (coding exon 5) of the CD6 gene. This alteration results from a C to A substitution at nucleotide position 932, causing the alanine (A) at amino acid position 311 to be replaced by a glutamic acid (E). 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