rs2296160
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000651.6(CR1):āc.7255A>Gā(p.Thr2419Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 1,593,392 control chromosomes in the GnomAD database, including 532,780 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000651.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CR1 | NM_000651.6 | c.7255A>G | p.Thr2419Ala | missense_variant, splice_region_variant | 44/47 | ENST00000367049.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CR1 | ENST00000367049.9 | c.7255A>G | p.Thr2419Ala | missense_variant, splice_region_variant | 44/47 | 5 | NM_000651.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.813 AC: 123577AN: 151992Hom.: 50449 Cov.: 31
GnomAD3 exomes AF: 0.819 AC: 187609AN: 228938Hom.: 77449 AF XY: 0.820 AC XY: 101209AN XY: 123444
GnomAD4 exome AF: 0.817 AC: 1177041AN: 1441282Hom.: 482295 Cov.: 32 AF XY: 0.818 AC XY: 585561AN XY: 715600
GnomAD4 genome ? AF: 0.813 AC: 123666AN: 152110Hom.: 50485 Cov.: 31 AF XY: 0.815 AC XY: 60604AN XY: 74374
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at