16-729386-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032304.4(HAGHL):c.779C>T(p.Pro260Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000439 in 1,526,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032304.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAGHL | NM_032304.4 | c.779C>T | p.Pro260Leu | missense_variant | 8/8 | ENST00000389703.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAGHL | ENST00000389703.8 | c.779C>T | p.Pro260Leu | missense_variant | 8/8 | 1 | NM_032304.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000339 AC: 4AN: 117922Hom.: 0 AF XY: 0.0000308 AC XY: 2AN XY: 65036
GnomAD4 exome AF: 0.0000429 AC: 59AN: 1374584Hom.: 0 Cov.: 33 AF XY: 0.0000428 AC XY: 29AN XY: 677642
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2022 | The c.779C>T (p.P260L) alteration is located in exon 8 (coding exon 8) of the HAGHL gene. This alteration results from a C to T substitution at nucleotide position 779, causing the proline (P) at amino acid position 260 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