12-66302620-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370285.1(HELB):c.17C>T(p.Pro6Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370285.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HELB | NM_001370285.1 | c.17C>T | p.Pro6Leu | missense_variant | Exon 1 of 13 | ENST00000247815.9 | NP_001357214.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HELB | ENST00000247815.9 | c.17C>T | p.Pro6Leu | missense_variant | Exon 1 of 13 | 1 | NM_001370285.1 | ENSP00000247815.5 | ||
HELB | ENST00000440906.6 | n.17C>T | non_coding_transcript_exon_variant | Exon 1 of 12 | 1 | ENSP00000396955.2 | ||||
HELB | ENST00000542394.5 | n.17C>T | non_coding_transcript_exon_variant | Exon 1 of 13 | 1 | ENSP00000439617.1 | ||||
HELB | ENST00000545134.1 | n.17C>T | non_coding_transcript_exon_variant | Exon 1 of 14 | 2 | ENSP00000443287.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251166Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135808
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461584Hom.: 0 Cov.: 29 AF XY: 0.0000289 AC XY: 21AN XY: 727072
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.17C>T (p.P6L) alteration is located in exon 1 (coding exon 1) of the HELB gene. This alteration results from a C to T substitution at nucleotide position 17, causing the proline (P) at amino acid position 6 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