1-220884492-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021958.4(HLX):āc.1255A>Cā(p.Ser419Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_021958.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLX | NM_021958.4 | c.1255A>C | p.Ser419Arg | missense_variant | 4/4 | ENST00000366903.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLX | ENST00000366903.8 | c.1255A>C | p.Ser419Arg | missense_variant | 4/4 | 1 | NM_021958.4 | P1 | |
HLX | ENST00000427693.1 | c.454A>C | p.Ter152= | incomplete_terminal_codon_variant, coding_sequence_variant | 4/4 | 3 | |||
HLX | ENST00000549319.2 | n.5062A>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248548Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134690
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461776Hom.: 0 Cov.: 33 AF XY: 0.0000344 AC XY: 25AN XY: 727192
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 19, 2022 | The c.1255A>C (p.S419R) alteration is located in exon 4 (coding exon 4) of the HLX gene. This alteration results from a A to C substitution at nucleotide position 1255, causing the serine (S) at amino acid position 419 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