16-16221677-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001171.6(ABCC6):c.191G>A(p.Arg64Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,558 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 Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R64W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001171.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.191G>A | p.Arg64Gln | missense_variant | Exon 2 of 31 | ENST00000205557.12 | NP_001162.5 | |
ABCC6 | NM_001079528.4 | c.191G>A | p.Arg64Gln | missense_variant | Exon 2 of 2 | NP_001072996.1 | ||
ABCC6 | NM_001351800.1 | c.-183G>A | 5_prime_UTR_variant | Exon 2 of 31 | NP_001338729.1 | |||
ABCC6 | NR_147784.1 | n.228G>A | non_coding_transcript_exon_variant | Exon 2 of 29 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152104Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461454Hom.: 0 Cov.: 32 AF XY: 0.0000330 AC XY: 24AN XY: 727020
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152104Hom.: 0 Cov.: 30 AF XY: 0.0000404 AC XY: 3AN XY: 74296
ClinVar
Submissions by phenotype
Autosomal recessive inherited pseudoxanthoma elasticum Uncertain:1
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not provided Uncertain:1
ABCC6: PM2, PP2, BP4 -
Autosomal recessive inherited pseudoxanthoma elasticum;C1867450:Pseudoxanthoma elasticum, forme fruste;C3276161:Arterial calcification, generalized, of infancy, 2 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at