rs3027878
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005334.3(HCFC1):c.4542G>T(p.Leu1514Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 1,178,047 control chromosomes in the GnomAD database, including 21,618 homozygotes. There are 75,804 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005334.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HCFC1 | ENST00000310441.12 | c.4542G>T | p.Leu1514Leu | synonymous_variant | Exon 19 of 26 | 1 | NM_005334.3 | ENSP00000309555.7 | ||
HCFC1 | ENST00000369984.4 | c.4674G>T | p.Leu1558Leu | synonymous_variant | Exon 19 of 26 | 5 | ENSP00000359001.4 | |||
HCFC1 | ENST00000444191.5 | c.264G>T | p.Leu88Leu | synonymous_variant | Exon 3 of 10 | 5 | ENSP00000399589.1 |
Frequencies
GnomAD3 genomes AF: 0.180 AC: 20308AN: 112628Hom.: 2176 Cov.: 25 AF XY: 0.194 AC XY: 6762AN XY: 34812
GnomAD3 exomes AF: 0.321 AC: 40409AN: 125834Hom.: 6675 AF XY: 0.335 AC XY: 13487AN XY: 40268
GnomAD4 exome AF: 0.185 AC: 196960AN: 1065364Hom.: 19444 Cov.: 32 AF XY: 0.199 AC XY: 69040AN XY: 346808
GnomAD4 genome AF: 0.180 AC: 20300AN: 112683Hom.: 2174 Cov.: 25 AF XY: 0.194 AC XY: 6764AN XY: 34877
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Methylmalonic acidemia with homocystinuria, type cblX Benign:2
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at