rs7536561
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_033343.4(LHX4):āc.983A>Gā(p.Asn328Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 1,613,834 control chromosomes in the GnomAD database, including 209,181 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_033343.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LHX4 | NM_033343.4 | c.983A>G | p.Asn328Ser | missense_variant | 6/6 | ENST00000263726.4 | |
LHX4-AS1 | NR_037642.1 | n.31+262T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LHX4 | ENST00000263726.4 | c.983A>G | p.Asn328Ser | missense_variant | 6/6 | 1 | NM_033343.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.420 AC: 63733AN: 151858Hom.: 15297 Cov.: 32
GnomAD3 exomes AF: 0.482 AC: 121287AN: 251416Hom.: 31656 AF XY: 0.502 AC XY: 68274AN XY: 135902
GnomAD4 exome AF: 0.509 AC: 744210AN: 1461858Hom.: 193892 Cov.: 63 AF XY: 0.514 AC XY: 373879AN XY: 727228
GnomAD4 genome ? AF: 0.419 AC: 63710AN: 151976Hom.: 15289 Cov.: 32 AF XY: 0.425 AC XY: 31560AN XY: 74264
ClinVar
Submissions by phenotype
Short stature-pituitary and cerebellar defects-small sella turcica syndrome Benign:3
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at