rs1063499
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000587.4(C7):āc.1166G>Cā(p.Ser389Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 1,612,408 control chromosomes in the GnomAD database, including 274,957 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000587.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C7 | NM_000587.4 | c.1166G>C | p.Ser389Thr | missense_variant | 10/18 | ENST00000313164.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C7 | ENST00000313164.10 | c.1166G>C | p.Ser389Thr | missense_variant | 10/18 | 1 | NM_000587.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.523 AC: 79420AN: 151914Hom.: 21760 Cov.: 32
GnomAD3 exomes AF: 0.575 AC: 142760AN: 248154Hom.: 41803 AF XY: 0.579 AC XY: 77926AN XY: 134646
GnomAD4 exome AF: 0.586 AC: 856107AN: 1460376Hom.: 253192 Cov.: 40 AF XY: 0.586 AC XY: 425484AN XY: 726488
GnomAD4 genome ? AF: 0.523 AC: 79457AN: 152032Hom.: 21765 Cov.: 32 AF XY: 0.527 AC XY: 39193AN XY: 74324
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 24, 2019 | - - |
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at