chr7-106004676-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152750.5(CDHR3):c.1041G>T(p.Lys347Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,614,004 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 (★).
Frequency
Consequence
NM_152750.5 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 |
---|---|---|---|---|---|---|---|
CDHR3 | NM_152750.5 | c.1041G>T | p.Lys347Asn | missense_variant | 8/19 | ENST00000317716.14 | |
CDHR3 | NM_001301161.2 | c.777G>T | p.Lys259Asn | missense_variant | 7/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDHR3 | ENST00000317716.14 | c.1041G>T | p.Lys347Asn | missense_variant | 8/19 | 1 | NM_152750.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249192Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135196
GnomAD4 exome AF: 0.0000705 AC: 103AN: 1461686Hom.: 0 Cov.: 31 AF XY: 0.0000701 AC XY: 51AN XY: 727120
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 05, 2023 | The c.1041G>T (p.K347N) alteration is located in exon 8 (coding exon 8) of the CDHR3 gene. This alteration results from a G to T substitution at nucleotide position 1041, causing the lysine (K) at amino acid position 347 to be replaced by an asparagine (N). 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