chr5-176575522-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017675.6(CDHR2):c.785C>T(p.Thr262Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,614,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T262S) has been classified as Uncertain significance.
Frequency
Consequence
NM_017675.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDHR2 | ENST00000261944.10 | c.785C>T | p.Thr262Met | missense_variant | Exon 10 of 32 | 1 | NM_017675.6 | ENSP00000261944.5 | ||
CDHR2 | ENST00000510636.5 | c.785C>T | p.Thr262Met | missense_variant | Exon 10 of 32 | 1 | ENSP00000424565.1 | |||
CDHR2 | ENST00000506348.1 | n.832C>T | non_coding_transcript_exon_variant | Exon 9 of 31 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251404Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135896
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461850Hom.: 0 Cov.: 37 AF XY: 0.0000481 AC XY: 35AN XY: 727232
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.785C>T (p.T262M) alteration is located in exon 10 (coding exon 9) of the CDHR2 gene. This alteration results from a C to T substitution at nucleotide position 785, causing the threonine (T) at amino acid position 262 to be replaced by a methionine (M). 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