3-108080081-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001777.4(CD47):c.310G>A(p.Asp104Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,460,992 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001777.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD47 | ENST00000361309.6 | c.310G>A | p.Asp104Asn | missense_variant | Exon 2 of 11 | 1 | NM_001777.4 | ENSP00000355361.5 | ||
CD47 | ENST00000355354.13 | c.310G>A | p.Asp104Asn | missense_variant | Exon 2 of 9 | 1 | ENSP00000347512.7 | |||
CD47 | ENST00000644850.1 | c.175G>A | p.Asp59Asn | missense_variant | Exon 2 of 5 | ENSP00000493750.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249060Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135132
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460992Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726772
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.310G>A (p.D104N) alteration is located in exon 2 (coding exon 2) of the CD47 gene. This alteration results from a G to A substitution at nucleotide position 310, causing the aspartic acid (D) at amino acid position 104 to be replaced by an asparagine (N). 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