rs72657699
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_001171.6(ABCC6):āc.955A>Gā(p.Ile319Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,612,760 control chromosomes in the GnomAD database, including 20 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 Benign (ā ā ).
Frequency
Consequence
NM_001171.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.955A>G | p.Ile319Val | missense_variant | 8/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.613A>G | p.Ile205Val | missense_variant | 8/31 | ||
ABCC6 | NR_147784.1 | n.992A>G | non_coding_transcript_exon_variant | 8/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.955A>G | p.Ile319Val | missense_variant | 8/31 | 1 | NM_001171.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00701 AC: 1065AN: 151980Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00127 AC: 318AN: 250582Hom.: 3 AF XY: 0.00111 AC XY: 150AN XY: 135504
GnomAD4 exome AF: 0.000406 AC: 593AN: 1460664Hom.: 12 Cov.: 32 AF XY: 0.000402 AC XY: 292AN XY: 726782
GnomAD4 genome ? AF: 0.00701 AC: 1066AN: 152096Hom.: 8 Cov.: 32 AF XY: 0.00699 AC XY: 520AN XY: 74378
ClinVar
Submissions by phenotype
Autosomal recessive inherited pseudoxanthoma elasticum Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Benign, criteria provided, single submitter | research | PXE International | Mar 01, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 15, 2019 | This variant is associated with the following publications: (PMID: 12384774, 16086317, 11536079) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Pseudoxanthoma elasticum, forme fruste Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Arterial calcification, generalized, of infancy, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at