rs4987682
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018646.6(TRPV6):āc.2162T>Cā(p.Met721Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 1,613,972 control chromosomes in the GnomAD database, including 15,697 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_018646.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPV6 | NM_018646.6 | c.2162T>C | p.Met721Thr | missense_variant | 15/15 | ENST00000359396.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPV6 | ENST00000359396.9 | c.2162T>C | p.Met721Thr | missense_variant | 15/15 | 1 | NM_018646.6 | P5 | |
TRPV6 | ENST00000485138.5 | n.1772T>C | non_coding_transcript_exon_variant | 9/9 | 2 | ||||
TRPV6 | ENST00000615386.4 | n.9803T>C | non_coding_transcript_exon_variant | 12/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.201 AC: 30573AN: 151994Hom.: 6395 Cov.: 33
GnomAD3 exomes AF: 0.0919 AC: 23113AN: 251440Hom.: 2993 AF XY: 0.0800 AC XY: 10877AN XY: 135894
GnomAD4 exome AF: 0.0834 AC: 121926AN: 1461860Hom.: 9283 Cov.: 31 AF XY: 0.0793 AC XY: 57702AN XY: 727230
GnomAD4 genome ? AF: 0.201 AC: 30636AN: 152112Hom.: 6414 Cov.: 33 AF XY: 0.193 AC XY: 14364AN XY: 74374
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
TRPV6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at