rs72664215
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001171.6(ABCC6):c.4403+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000934 in 1,605,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
ABCC6
NM_001171.6 intron
NM_001171.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.347
Genes affected
ABCC6 (HGNC:57): (ATP binding cassette subfamily C member 6) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). The encoded protein, a member of the MRP subfamily, is involved in multi-drug resistance. Mutations in this gene cause pseudoxanthoma elasticum. Alternatively spliced transcript variants that encode different proteins have been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.4403+11C>T | intron_variant | ENST00000205557.12 | NP_001162.5 | |||
ABCC6 | NM_001351800.1 | c.4061+11C>T | intron_variant | NP_001338729.1 | ||||
ABCC6 | NR_147784.1 | n.4065+11C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.4403+11C>T | intron_variant | 1 | NM_001171.6 | ENSP00000205557 | P1 | |||
ABCC6 | ENST00000456970.6 | c.*1412+11C>T | intron_variant, NMD_transcript_variant | 2 | ENSP00000405002 | |||||
ABCC6 | ENST00000622290.5 | c.*575+11C>T | intron_variant, NMD_transcript_variant | 5 | ENSP00000483331 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244572Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 132938
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GnomAD4 exome AF: 0.00000895 AC: 13AN: 1453070Hom.: 0 Cov.: 34 AF XY: 0.0000111 AC XY: 8AN XY: 721218
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74364
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
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DANN
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RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at