rs8058694
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1
The NM_001171.6(ABCC6):c.1896C>A(p.His632Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 1,608,938 control chromosomes in the GnomAD database, including 178,917 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
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.1896C>A | p.His632Gln | missense_variant | 15/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.1554C>A | p.His518Gln | missense_variant | 15/31 | ||
ABCC6 | NR_147784.1 | n.1933C>A | non_coding_transcript_exon_variant | 15/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.1896C>A | p.His632Gln | missense_variant | 15/31 | 1 | NM_001171.6 | P1 | |
ABCC6 | ENST00000622290.5 | c.1896C>A | p.His632Gln | missense_variant, NMD_transcript_variant | 15/32 | 5 | |||
ABCC6 | ENST00000456970.6 | c.1896C>A | p.His632Gln | missense_variant, NMD_transcript_variant | 15/29 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.427 AC: 64716AN: 151590Hom.: 14342 Cov.: 31
GnomAD3 exomes AF: 0.419 AC: 105156AN: 251100Hom.: 23455 AF XY: 0.413 AC XY: 56008AN XY: 135740
GnomAD4 exome AF: 0.468 AC: 681571AN: 1457230Hom.: 164574 Cov.: 52 AF XY: 0.461 AC XY: 334447AN XY: 725092
GnomAD4 genome ? AF: 0.427 AC: 64726AN: 151708Hom.: 14343 Cov.: 31 AF XY: 0.417 AC XY: 30888AN XY: 74128
ClinVar
Submissions by phenotype
Autosomal recessive inherited pseudoxanthoma elasticum Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Benign, criteria provided, single submitter | research | PXE International | Mar 01, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Pseudoxanthoma elasticum, forme fruste Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Arterial calcification, generalized, of infancy, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at