1-112456310-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018704.3(CTTNBP2NL):āc.818T>Cā(p.Ile273Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000282 in 1,613,782 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018704.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTTNBP2NL | NM_018704.3 | c.818T>C | p.Ile273Thr | missense_variant | 6/6 | ENST00000271277.11 | NP_061174.1 | |
CTTNBP2NL | XM_011541781.3 | c.818T>C | p.Ile273Thr | missense_variant | 6/6 | XP_011540083.1 | ||
CTTNBP2NL | XM_017001806.2 | c.818T>C | p.Ile273Thr | missense_variant | 6/6 | XP_016857295.1 | ||
CTTNBP2NL | XM_047425362.1 | c.818T>C | p.Ile273Thr | missense_variant | 6/6 | XP_047281318.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151882Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 40AN: 249958Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135436
GnomAD4 exome AF: 0.000306 AC: 447AN: 1461782Hom.: 1 Cov.: 32 AF XY: 0.000298 AC XY: 217AN XY: 727188
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152000Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.818T>C (p.I273T) alteration is located in exon 6 (coding exon 4) of the CTTNBP2NL gene. This alteration results from a T to C substitution at nucleotide position 818, causing the isoleucine (I) at amino acid position 273 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