1-180248376-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_033343.4(LHX4):c.168G>A(p.Lys56=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,264 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 Likely benign (★).
Frequency
Consequence
NM_033343.4 synonymous
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 |
---|---|---|---|---|---|---|---|
LHX4 | NM_033343.4 | c.168G>A | p.Lys56= | synonymous_variant | 2/6 | ENST00000263726.4 | |
LHX4 | XM_011510105.3 | c.-16G>A | 5_prime_UTR_variant | 2/6 | |||
LHX4 | XM_011510106.4 | c.-16G>A | 5_prime_UTR_variant | 2/6 | |||
LHX4 | XM_011510108.3 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHX4 | ENST00000263726.4 | c.168G>A | p.Lys56= | synonymous_variant | 2/6 | 1 | NM_033343.4 | P1 | |
LHX4 | ENST00000558139.1 | n.400G>A | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
LHX4 | ENST00000561113.1 | c.94G>A | p.Val32Met | missense_variant, NMD_transcript_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152268Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727240
GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152386Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74518
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 22, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.