rs77081173
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001195263.2(PDZD7):c.2157C>T(p.Asp719Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.003 in 1,295,638 control chromosomes in the GnomAD database, including 96 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001195263.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDZD7 | ENST00000619208.6 | c.2157C>T | p.Asp719Asp | synonymous_variant | Exon 15 of 17 | 5 | NM_001195263.2 | ENSP00000480489.1 | ||
PDZD7 | ENST00000474125.7 | n.*2104C>T | non_coding_transcript_exon_variant | Exon 11 of 13 | 2 | ENSP00000474447.1 | ||||
PDZD7 | ENST00000474125.7 | n.*2104C>T | 3_prime_UTR_variant | Exon 11 of 13 | 2 | ENSP00000474447.1 |
Frequencies
GnomAD3 genomes AF: 0.0140 AC: 1977AN: 141412Hom.: 47 Cov.: 25
GnomAD3 exomes AF: 0.00295 AC: 382AN: 129398Hom.: 7 AF XY: 0.00250 AC XY: 177AN XY: 70906
GnomAD4 exome AF: 0.00165 AC: 1907AN: 1154128Hom.: 49 Cov.: 40 AF XY: 0.00140 AC XY: 799AN XY: 569220
GnomAD4 genome AF: 0.0140 AC: 1983AN: 141510Hom.: 47 Cov.: 25 AF XY: 0.0130 AC XY: 891AN XY: 68296
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
Asp719Asp in Exon 15 of PDZD7: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 15.3% (18/118) of ch romosomes from a population in the dbSNP database (http://www.ncbi.nlm.nih.gov/p rojects/SNP; rs77081173). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at