11-62663143-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024099.5(LBHD1):c.778G>A(p.Ala260Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024099.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LBHD1 | NM_024099.5 | c.778G>A | p.Ala260Thr | missense_variant | Exon 7 of 7 | ENST00000354588.8 | NP_077004.2 | |
C11orf98 | NM_001286086.2 | c.279G>A | p.Lys93Lys | synonymous_variant | Exon 4 of 4 | ENST00000524958.6 | NP_001273015.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LBHD1 | ENST00000354588.8 | c.778G>A | p.Ala260Thr | missense_variant | Exon 7 of 7 | 1 | NM_024099.5 | ENSP00000346600.3 | ||
C11orf98 | ENST00000524958.6 | c.279G>A | p.Lys93Lys | synonymous_variant | Exon 4 of 4 | 2 | NM_001286086.2 | ENSP00000432523.2 | ||
ENSG00000255432 | ENST00000528405.1 | c.262+93G>A | intron_variant | Intron 3 of 3 | 4 | ENSP00000435188.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461836Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 727212
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.778G>A (p.A260T) alteration is located in exon 7 (coding exon 6) of the LBHD1 gene. This alteration results from a G to A substitution at nucleotide position 778, causing the alanine (A) at amino acid position 260 to be replaced by a threonine (T). 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