6-138404563-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014320.3(HEBP2):c.68C>T(p.Pro23Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,096 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014320.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HEBP2 | NM_014320.3 | c.68C>T | p.Pro23Leu | missense_variant | Exon 1 of 4 | ENST00000607197.6 | NP_055135.1 | |
HEBP2 | NM_001326381.2 | c.68C>T | p.Pro23Leu | missense_variant | Exon 1 of 4 | NP_001313310.1 | ||
HEBP2 | NM_001326380.2 | c.136-582C>T | intron_variant | Intron 1 of 3 | NP_001313309.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HEBP2 | ENST00000607197.6 | c.68C>T | p.Pro23Leu | missense_variant | Exon 1 of 4 | 1 | NM_014320.3 | ENSP00000475750.1 | ||
HEBP2 | ENST00000367697.7 | c.68C>T | p.Pro23Leu | missense_variant | Exon 1 of 4 | 2 | ENSP00000356670.3 | |||
HEBP2 | ENST00000448741.5 | c.136-582C>T | intron_variant | Intron 1 of 3 | 5 | ENSP00000392101.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1158082Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 559334
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.68C>T (p.P23L) alteration is located in exon 1 (coding exon 1) of the HEBP2 gene. This alteration results from a C to T substitution at nucleotide position 68, causing the proline (P) at amino acid position 23 to be replaced by a leucine (L). 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