rs3738182
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_021958.4(HLX):c.1083G>A(p.Glu361=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,613,072 control chromosomes in the GnomAD database, including 30,795 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 3247 hom., cov: 32)
Exomes 𝑓: 0.19 ( 27548 hom. )
Consequence
HLX
NM_021958.4 synonymous
NM_021958.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.372
Genes affected
HLX (HGNC:4978): (H2.0 like homeobox) Enables sequence-specific DNA binding activity. Predicted to be involved in cell differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including animal organ development; enteric nervous system development; and regulation of T-helper cell differentiation. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
?
Synonymous conserved (PhyloP=0.372 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLX | NM_021958.4 | c.1083G>A | p.Glu361= | synonymous_variant | 4/4 | ENST00000366903.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLX | ENST00000366903.8 | c.1083G>A | p.Glu361= | synonymous_variant | 4/4 | 1 | NM_021958.4 | P1 | |
HLX | ENST00000427693.1 | c.282G>A | p.Glu94= | synonymous_variant | 4/4 | 3 | |||
HLX | ENST00000549319.2 | n.4890G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.202 AC: 30733AN: 151858Hom.: 3244 Cov.: 32
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GnomAD3 exomes AF: 0.183 AC: 45529AN: 249050Hom.: 4392 AF XY: 0.183 AC XY: 24722AN XY: 134928
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GnomAD4 exome AF: 0.191 AC: 279767AN: 1461096Hom.: 27548 Cov.: 41 AF XY: 0.191 AC XY: 138834AN XY: 726802
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GnomAD4 genome ? AF: 0.202 AC: 30749AN: 151976Hom.: 3247 Cov.: 32 AF XY: 0.201 AC XY: 14941AN XY: 74274
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at