chr21-39423029-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152505.4(LCA5L):c.784C>G(p.His262Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000404 in 1,461,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152505.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCA5L | NM_152505.4 | c.784C>G | p.His262Asp | missense_variant | 6/11 | ENST00000288350.8 | |
GET1-SH3BGR | NR_146618.2 | n.920-2731G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCA5L | ENST00000288350.8 | c.784C>G | p.His262Asp | missense_variant | 6/11 | 5 | NM_152505.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251334Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135852
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461738Hom.: 0 Cov.: 32 AF XY: 0.0000330 AC XY: 24AN XY: 727176
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2021 | The c.784C>G (p.H262D) alteration is located in exon 5 (coding exon 2) of the LCA5L gene. This alteration results from a C to G substitution at nucleotide position 784, causing the histidine (H) at amino acid position 262 to be replaced by an aspartic acid (D). 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