chr21-39410059-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152505.4(LCA5L):c.1202A>G(p.Lys401Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,611,650 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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
Genome browser will be placed here
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.1202A>G | p.Lys401Arg | missense_variant | 10/11 | ENST00000288350.8 | |
GET1-SH3BGR | NR_146618.2 | n.826-785T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCA5L | ENST00000288350.8 | c.1202A>G | p.Lys401Arg | missense_variant | 10/11 | 5 | NM_152505.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000280 AC: 70AN: 250204Hom.: 0 AF XY: 0.000281 AC XY: 38AN XY: 135180
GnomAD4 exome AF: 0.000168 AC: 245AN: 1459308Hom.: 0 Cov.: 29 AF XY: 0.000178 AC XY: 129AN XY: 726016
GnomAD4 genome ? AF: 0.000249 AC: 38AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.1202A>G (p.K401R) alteration is located in exon 9 (coding exon 6) of the LCA5L gene. This alteration results from a A to G substitution at nucleotide position 1202, causing the lysine (K) at amino acid position 401 to be replaced by an arginine (R). 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