6-43509619-G-T
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001012974.4(LRRC73):c.167C>A(p.Thr56Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,452,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T56A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001012974.4 missense
Scores
Clinical Significance
Conservation
Publications
- hypomyelinating leukodystrophy 11Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- Treacher Collins syndrome 3Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen
- Treacher-Collins syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- hypomyelination-hypogonadotropic hypogonadism-hypodontia syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1452664Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 722224 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.167C>A (p.T56K) alteration is located in exon 1 (coding exon 1) of the LRRC73 gene. This alteration results from a C to A substitution at nucleotide position 167, causing the threonine (T) at amino acid position 56 to be replaced by a lysine (K). 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