chr18-74291863-A-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_148923.4(CYB5A):c.13T>G(p.Ser5Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000528 in 1,612,202 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_148923.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYB5A | NM_148923.4 | c.13T>G | p.Ser5Ala | missense_variant | 1/5 | ENST00000340533.9 | |
CYB5A | NM_001190807.3 | c.13T>G | p.Ser5Ala | missense_variant | 1/4 | ||
CYB5A | NM_001914.4 | c.13T>G | p.Ser5Ala | missense_variant | 1/6 | ||
CYB5A | XM_011525835.3 | c.13T>G | p.Ser5Ala | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYB5A | ENST00000340533.9 | c.13T>G | p.Ser5Ala | missense_variant | 1/5 | 1 | NM_148923.4 | P1 | |
CYB5A | ENST00000494131.6 | c.13T>G | p.Ser5Ala | missense_variant | 1/6 | 1 | |||
CYB5A | ENST00000397914.4 | c.13T>G | p.Ser5Ala | missense_variant | 1/4 | 3 | |||
CYB5A | ENST00000583418.1 | n.95T>G | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00303 AC: 459AN: 151282Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000749 AC: 188AN: 251016Hom.: 1 AF XY: 0.000501 AC XY: 68AN XY: 135740
GnomAD4 exome AF: 0.000269 AC: 393AN: 1460802Hom.: 3 Cov.: 32 AF XY: 0.000215 AC XY: 156AN XY: 726772
GnomAD4 genome ? AF: 0.00303 AC: 459AN: 151400Hom.: 4 Cov.: 32 AF XY: 0.00300 AC XY: 222AN XY: 73922
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 16, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Aug 24, 2015 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at