10-96024866-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001349008.3(CC2D2B):āc.3902T>Cā(p.Ile1301Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000731 in 1,368,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001349008.3 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 |
---|---|---|---|---|---|---|---|
CC2D2B | NM_001349008.3 | c.3902T>C | p.Ile1301Thr | missense_variant | 33/35 | ENST00000646931.3 | |
ENTPD1-AS1 | NR_038444.1 | n.296+64400A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CC2D2B | ENST00000646931.3 | c.3902T>C | p.Ile1301Thr | missense_variant | 33/35 | NM_001349008.3 | P1 | ||
ENTPD1-AS1 | ENST00000669711.1 | n.300+64400A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 7.31e-7 AC: 1AN: 1368028Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 676062
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.794T>C (p.I265T) alteration is located in exon 10 (coding exon 8) of the CC2D2B gene. This alteration results from a T to C substitution at nucleotide position 794, causing the isoleucine (I) at amino acid position 265 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.