11-12504399-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018222.5(PARVA):c.627C>A(p.Asp209Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,460,740 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_018222.5 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 |
---|---|---|---|---|---|---|---|---|---|---|
PARVA | ENST00000334956.15 | c.627C>A | p.Asp209Glu | missense_variant | Exon 6 of 13 | 1 | NM_018222.5 | ENSP00000334008.9 | ||
PARVA | ENST00000528916.1 | c.519C>A | p.Asp173Glu | missense_variant | Exon 6 of 8 | 5 | ENSP00000435860.1 | |||
PARVA | ENST00000533345.5 | n.604C>A | non_coding_transcript_exon_variant | Exon 6 of 8 | 5 | |||||
PARVA | ENST00000533392.1 | n.*44C>A | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1460740Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 726694
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.747C>A (p.D249E) alteration is located in exon 6 (coding exon 6) of the PARVA gene. This alteration results from a C to A substitution at nucleotide position 747, causing the aspartic acid (D) at amino acid position 249 to be replaced by a glutamic acid (E). 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