X-153949402-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_005334.3(HCFC1):c.6069-16T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 1,199,638 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005334.3 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.6069-16T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.6069-16T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005334.3 | P2 | |||
HCFC1 | ENST00000369984.4 | c.6204-16T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | A2 | ||||
HCFC1 | ENST00000444191.5 | c.1795-16T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000903 AC: 1AN: 110728Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 32962
GnomAD4 exome AF: 0.0000138 AC: 15AN: 1088910Hom.: 0 Cov.: 29 AF XY: 0.00000564 AC XY: 2AN XY: 354856
GnomAD4 genome ? AF: 0.00000903 AC: 1AN: 110728Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 32962
ClinVar
Submissions by phenotype
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at