rs41278174
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_001171.6(ABCC6):c.3190C>T(p.Arg1064Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 1,613,760 control chromosomes in the GnomAD database, including 587 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.3190C>T | p.Arg1064Trp | missense_variant | Exon 23 of 31 | ENST00000205557.12 | NP_001162.5 | |
ABCC6 | NM_001351800.1 | c.2848C>T | p.Arg950Trp | missense_variant | Exon 23 of 31 | NP_001338729.1 | ||
ABCC6 | NR_147784.1 | n.3052C>T | non_coding_transcript_exon_variant | Exon 22 of 29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.3190C>T | p.Arg1064Trp | missense_variant | Exon 23 of 31 | 1 | NM_001171.6 | ENSP00000205557.7 | ||
ABCC6 | ENST00000456970.6 | n.*399C>T | non_coding_transcript_exon_variant | Exon 22 of 29 | 2 | ENSP00000405002.2 | ||||
ABCC6 | ENST00000622290.5 | n.3190C>T | non_coding_transcript_exon_variant | Exon 23 of 32 | 5 | ENSP00000483331.2 | ||||
ABCC6 | ENST00000456970.6 | n.*399C>T | 3_prime_UTR_variant | Exon 22 of 29 | 2 | ENSP00000405002.2 |
Frequencies
GnomAD3 genomes AF: 0.0175 AC: 2669AN: 152218Hom.: 34 Cov.: 33
GnomAD3 exomes AF: 0.0207 AC: 5197AN: 251186Hom.: 78 AF XY: 0.0216 AC XY: 2940AN XY: 135888
GnomAD4 exome AF: 0.0248 AC: 36279AN: 1461424Hom.: 553 Cov.: 33 AF XY: 0.0250 AC XY: 18157AN XY: 726986
GnomAD4 genome AF: 0.0175 AC: 2670AN: 152336Hom.: 34 Cov.: 33 AF XY: 0.0182 AC XY: 1358AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:5
This variant is associated with the following publications: (PMID: 31456290, 16086317, 25264593) -
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ABCC6: BS1, BS2 -
Autosomal recessive inherited pseudoxanthoma elasticum Pathogenic:1Benign:3
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not specified Benign:4
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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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Autosomal recessive inherited pseudoxanthoma elasticum;C1867450:Pseudoxanthoma elasticum, forme fruste;C3276161:Arterial calcification, generalized, of infancy, 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at