chr17-16428313-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_016113.5(TRPV2):c.1351-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,614,108 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_016113.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPV2 | NM_016113.5 | c.1351-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000338560.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPV2 | ENST00000338560.12 | c.1351-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016113.5 | P1 | |||
ENST00000441875.1 | n.75-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 | ||||||
TRPV2 | ENST00000583241.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000894 AC: 136AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00272 AC: 683AN: 251446Hom.: 4 AF XY: 0.00275 AC XY: 374AN XY: 135900
GnomAD4 exome AF: 0.00109 AC: 1589AN: 1461802Hom.: 14 Cov.: 32 AF XY: 0.00128 AC XY: 934AN XY: 727222
GnomAD4 genome ? AF: 0.000900 AC: 137AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000967 AC XY: 72AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at