rs72657689
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM1
The NM_001171.6(ABCC6):c.2848G>A(p.Ala950Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000301 in 1,579,638 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001171.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.2848G>A | p.Ala950Thr | missense_variant | Exon 22 of 31 | ENST00000205557.12 | NP_001162.5 | |
ABCC6 | NM_001351800.1 | c.2506G>A | p.Ala836Thr | missense_variant | Exon 22 of 31 | NP_001338729.1 | ||
ABCC6 | NR_147784.1 | n.2710G>A | non_coding_transcript_exon_variant | Exon 21 of 29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.2848G>A | p.Ala950Thr | missense_variant | Exon 22 of 31 | 1 | NM_001171.6 | ENSP00000205557.7 | ||
ABCC6 | ENST00000456970.6 | n.*57G>A | non_coding_transcript_exon_variant | Exon 21 of 29 | 2 | ENSP00000405002.2 | ||||
ABCC6 | ENST00000622290.5 | n.2848G>A | non_coding_transcript_exon_variant | Exon 22 of 32 | 5 | ENSP00000483331.2 | ||||
ABCC6 | ENST00000456970.6 | n.*57G>A | 3_prime_UTR_variant | Exon 21 of 29 | 2 | ENSP00000405002.2 |
Frequencies
GnomAD3 genomes AF: 0.000361 AC: 55AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000551 AC: 104AN: 188620Hom.: 0 AF XY: 0.000562 AC XY: 57AN XY: 101428
GnomAD4 exome AF: 0.000294 AC: 419AN: 1427326Hom.: 1 Cov.: 33 AF XY: 0.000320 AC XY: 226AN XY: 706934
GnomAD4 genome AF: 0.000368 AC: 56AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.000376 AC XY: 28AN XY: 74470
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
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This variant is associated with the following publications: (PMID: 17617515, 23485117) -
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Autosomal recessive inherited pseudoxanthoma elasticum Uncertain:1Benign:1
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Pseudoxanthoma elasticum, forme fruste Benign:1
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Arterial calcification, generalized, of infancy, 2 Benign:1
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ABCC6-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at