NM_017675.6:c.740C>T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017675.6(CDHR2):c.740C>T(p.Ser247Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,226 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.740C>T | p.Ser247Leu | missense_variant | Exon 9 of 32 | 1 | NM_017675.6 | ENSP00000261944.5 | ||
CDHR2 | ENST00000510636.5 | c.740C>T | p.Ser247Leu | missense_variant | Exon 9 of 32 | 1 | ENSP00000424565.1 | |||
CDHR2 | ENST00000506348.1 | n.787C>T | non_coding_transcript_exon_variant | Exon 8 of 31 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251356Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135880
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461884Hom.: 0 Cov.: 37 AF XY: 0.0000151 AC XY: 11AN XY: 727240
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.740C>T (p.S247L) alteration is located in exon 9 (coding exon 8) of the CDHR2 gene. This alteration results from a C to T substitution at nucleotide position 740, causing the serine (S) at amino acid position 247 to be replaced by a leucine (L). 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