rs59002125
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM1BP4_StrongBP6_Very_Strong
The NM_001171.6(ABCC6):c.1990C>T(p.Pro664Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000206 in 1,613,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P664T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001171.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.1990C>T | p.Pro664Ser | missense_variant | 16/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.1648C>T | p.Pro550Ser | missense_variant | 16/31 | ||
ABCC6 | NR_147784.1 | n.2027C>T | non_coding_transcript_exon_variant | 16/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.1990C>T | p.Pro664Ser | missense_variant | 16/31 | 1 | NM_001171.6 | P1 | |
ABCC6 | ENST00000622290.5 | c.1990C>T | p.Pro664Ser | missense_variant, NMD_transcript_variant | 16/32 | 5 | |||
ABCC6 | ENST00000456970.6 | c.1990C>T | p.Pro664Ser | missense_variant, NMD_transcript_variant | 16/29 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 151972Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000482 AC: 120AN: 249032Hom.: 1 AF XY: 0.000490 AC XY: 66AN XY: 134816
GnomAD4 exome AF: 0.000196 AC: 286AN: 1461886Hom.: 0 Cov.: 35 AF XY: 0.000208 AC XY: 151AN XY: 727246
GnomAD4 genome AF: 0.000309 AC: 47AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74322
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | ABCC6: BP4 - |
Autosomal recessive inherited pseudoxanthoma elasticum Uncertain:1
Uncertain significance, no assertion criteria provided | research | PXE International | Mar 01, 2021 | - - |
Autosomal recessive inherited pseudoxanthoma elasticum;C1867450:Pseudoxanthoma elasticum, forme fruste;C3276161:Arterial calcification, generalized, of infancy, 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at