chr17-48543231-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002145.4(HOXB2):āc.908T>Cā(p.Phe303Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000515 in 1,613,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002145.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXB2 | NM_002145.4 | c.908T>C | p.Phe303Ser | missense_variant | 2/2 | ENST00000330070.6 | |
HOXB2 | XM_005257275.5 | c.581T>C | p.Phe194Ser | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXB2 | ENST00000330070.6 | c.908T>C | p.Phe303Ser | missense_variant | 2/2 | 1 | NM_002145.4 | P1 | |
HOXB2 | ENST00000571287.1 | n.553T>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151956Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249250Hom.: 0 AF XY: 0.0000816 AC XY: 11AN XY: 134868
GnomAD4 exome AF: 0.0000541 AC: 79AN: 1460966Hom.: 0 Cov.: 33 AF XY: 0.0000688 AC XY: 50AN XY: 726680
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152074Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2023 | The c.908T>C (p.F303S) alteration is located in exon 2 (coding exon 2) of the HOXB2 gene. This alteration results from a T to C substitution at nucleotide position 908, causing the phenylalanine (F) at amino acid position 303 to be replaced by a serine (S). 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