7-142908736-C-T
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The ENST00000265310.6(TRPV5):c.1968G>A(p.Lys656=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
TRPV5
ENST00000265310.6 synonymous
ENST00000265310.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0180
Genes affected
TRPV5 (HGNC:3145): (transient receptor potential cation channel subfamily V member 5) This gene is a member of the transient receptor family and the TrpV subfamily. The calcium-selective channel encoded by this gene has 6 transmembrane-spanning domains, multiple potential phosphorylation sites, an N-linked glycosylation site, and 5 ANK repeats. This protein forms homotetramers or heterotetramers and is activated by a low internal calcium level. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP7
Synonymous conserved (PhyloP=0.018 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TRPV5 | NM_019841.7 | c.1968G>A | p.Lys656= | synonymous_variant | 15/15 | ENST00000265310.6 | NP_062815.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TRPV5 | ENST00000265310.6 | c.1968G>A | p.Lys656= | synonymous_variant | 15/15 | 1 | NM_019841.7 | ENSP00000265310 | P1 | |
| TRPV5 | ENST00000439304.5 | c.1803G>A | p.Lys601= | synonymous_variant | 14/14 | 5 | ENSP00000406361 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461834Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727222
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GnomAD4 genome 0.00000657 AC: 1AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74484
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Uncertain:1
| Uncertain significance, no assertion criteria provided | literature only | Martin Pollak Laboratory, Beth Israel Deaconess Medical Center | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at