rs201260214
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_145038.5(DRC1):āc.2075C>Gā(p.Thr692Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000447 in 1,614,048 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T692T) has been classified as Likely benign.
Frequency
Consequence
NM_145038.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DRC1 | NM_145038.5 | c.2075C>G | p.Thr692Ser | missense_variant | 16/17 | ENST00000288710.7 | |
DRC1 | XM_047446339.1 | c.1055C>G | p.Thr352Ser | missense_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DRC1 | ENST00000288710.7 | c.2075C>G | p.Thr692Ser | missense_variant | 16/17 | 2 | NM_145038.5 | P1 | |
DRC1 | ENST00000649059.1 | c.*1038C>G | 3_prime_UTR_variant, NMD_transcript_variant | 15/16 |
Frequencies
GnomAD3 genomes ? AF: 0.000362 AC: 55AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000330 AC: 83AN: 251384Hom.: 1 AF XY: 0.000316 AC XY: 43AN XY: 135876
GnomAD4 exome AF: 0.000456 AC: 666AN: 1461858Hom.: 1 Cov.: 32 AF XY: 0.000426 AC XY: 310AN XY: 727232
GnomAD4 genome ? AF: 0.000361 AC: 55AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74416
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 21 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 16, 2022 | The DRC1 c.2075C>G; p.Thr692Ser variant (rs201260214), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 525259). This variant is found in the general population with an allele frequency of 0.033% (92/282,772 alleles, including 1 homozygote) in the Genome Aggregation Database. The threonine at codon 692 is moderately conserved, but computational analyses predict that this variant is neutral (REVEL: 0.04). However, given the lack of clinical and functional data, the significance of the p.Thr692Ser variant is uncertain at this time. - |
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at