chr17-55315408-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_002126.5(HLF):c.633C>G(p.Ile211Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,850 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I211F) has been classified as Uncertain significance.
Frequency
Consequence
NM_002126.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLF | NM_002126.5 | c.633C>G | p.Ile211Met | missense_variant | 3/4 | ENST00000226067.10 | |
HLF | NM_001330375.2 | c.378C>G | p.Ile126Met | missense_variant | 3/4 | ||
HLF | XM_005257269.3 | c.633C>G | p.Ile211Met | missense_variant | 3/4 | ||
HLF | XM_047435895.1 | c.378C>G | p.Ile126Met | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLF | ENST00000226067.10 | c.633C>G | p.Ile211Met | missense_variant | 3/4 | 1 | NM_002126.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251246Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135774
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461850Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727238
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.633C>G (p.I211M) alteration is located in exon 3 (coding exon 3) of the HLF gene. This alteration results from a C to G substitution at nucleotide position 633, causing the isoleucine (I) at amino acid position 211 to be replaced by a methionine (M). 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