chrX-153949391-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005334.3(HCFC1):c.6069-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000699 in 1,202,368 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 40 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005334.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCFC1 | NM_005334.3 | c.6069-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000310441.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.6069-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005334.3 | P2 | |||
HCFC1 | ENST00000369984.4 | c.6204-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | A2 | ||||
HCFC1 | ENST00000444191.5 | c.1795-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000451 AC: 5AN: 110914Hom.: 0 Cov.: 23 AF XY: 0.0000906 AC XY: 3AN XY: 33110
GnomAD3 exomes AF: 0.000144 AC: 26AN: 180058Hom.: 0 AF XY: 0.000241 AC XY: 16AN XY: 66300
GnomAD4 exome AF: 0.0000724 AC: 79AN: 1091454Hom.: 0 Cov.: 29 AF XY: 0.000104 AC XY: 37AN XY: 357346
GnomAD4 genome AF: 0.0000451 AC: 5AN: 110914Hom.: 0 Cov.: 23 AF XY: 0.0000906 AC XY: 3AN XY: 33110
ClinVar
Submissions by phenotype
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at