rs781089161
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The NM_015214.3(DDHD2):c.335G>A(p.Arg112Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,146 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R112L) has been classified as Uncertain significance.
Frequency
Consequence
NM_015214.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDHD2 | NM_015214.3 | c.335G>A | p.Arg112Gln | missense_variant | 3/18 | ENST00000397166.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDHD2 | ENST00000397166.7 | c.335G>A | p.Arg112Gln | missense_variant | 3/18 | 2 | NM_015214.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000212 AC: 53AN: 250398Hom.: 0 AF XY: 0.000192 AC XY: 26AN XY: 135420
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1460986Hom.: 0 Cov.: 31 AF XY: 0.0000330 AC XY: 24AN XY: 726834
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 54 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 05, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at