chr12-6816128-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000616.5(CD4):āc.680T>Cā(p.Phe227Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00402 in 1,614,104 control chromosomes in the GnomAD database, including 185 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000616.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD4 | NM_000616.5 | c.680T>C | p.Phe227Ser | missense_variant | 6/10 | ENST00000011653.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD4 | ENST00000011653.9 | c.680T>C | p.Phe227Ser | missense_variant | 6/10 | 1 | NM_000616.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0206 AC: 3130AN: 152108Hom.: 96 Cov.: 32
GnomAD3 exomes AF: 0.00526 AC: 1322AN: 251478Hom.: 40 AF XY: 0.00363 AC XY: 493AN XY: 135912
GnomAD4 exome AF: 0.00229 AC: 3354AN: 1461878Hom.: 89 Cov.: 34 AF XY: 0.00197 AC XY: 1435AN XY: 727244
GnomAD4 genome AF: 0.0206 AC: 3139AN: 152226Hom.: 96 Cov.: 32 AF XY: 0.0200 AC XY: 1490AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at