rs72664283
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001171.6(ABCC6):āc.1077A>Gā(p.Ser359=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00374 in 1,610,970 control chromosomes in the GnomAD database, including 112 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. S359S) has been classified as Likely benign.
Frequency
Consequence
NM_001171.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.1077A>G | p.Ser359= | synonymous_variant | 9/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.735A>G | p.Ser245= | synonymous_variant | 9/31 | ||
ABCC6 | NR_147784.1 | n.1114A>G | non_coding_transcript_exon_variant | 9/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.1077A>G | p.Ser359= | synonymous_variant | 9/31 | 1 | NM_001171.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0133 AC: 2023AN: 152108Hom.: 38 Cov.: 31
GnomAD3 exomes AF: 0.00559 AC: 1402AN: 250716Hom.: 21 AF XY: 0.00526 AC XY: 713AN XY: 135482
GnomAD4 exome AF: 0.00274 AC: 4001AN: 1458746Hom.: 74 Cov.: 32 AF XY: 0.00295 AC XY: 2142AN XY: 725700
GnomAD4 genome AF: 0.0133 AC: 2031AN: 152224Hom.: 38 Cov.: 31 AF XY: 0.0138 AC XY: 1031AN XY: 74442
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, no assertion criteria provided | research | PXE International | Mar 01, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 19, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at