rs376049260
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_005334.3(HCFC1):c.3492C>T(p.Ser1164Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,169,225 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 414 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005334.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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HCFC1 | ENST00000310441.12 | c.3492C>T | p.Ser1164Ser | synonymous_variant | Exon 17 of 26 | 1 | NM_005334.3 | ENSP00000309555.7 | ||
HCFC1 | ENST00000369984.4 | c.3492C>T | p.Ser1164Ser | synonymous_variant | Exon 17 of 26 | 5 | ENSP00000359001.4 |
Frequencies
GnomAD3 genomes AF: 0.000792 AC: 89AN: 112331Hom.: 0 Cov.: 24 AF XY: 0.000840 AC XY: 29AN XY: 34519
GnomAD3 exomes AF: 0.000666 AC: 80AN: 120161Hom.: 0 AF XY: 0.000710 AC XY: 23AN XY: 32401
GnomAD4 exome AF: 0.00109 AC: 1152AN: 1056841Hom.: 0 Cov.: 34 AF XY: 0.00113 AC XY: 385AN XY: 340155
GnomAD4 genome AF: 0.000792 AC: 89AN: 112384Hom.: 0 Cov.: 24 AF XY: 0.000839 AC XY: 29AN XY: 34582
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:3
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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. -
HCFC1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Methylmalonic acidemia with homocystinuria, type cblX Benign:1
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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