rs57745014
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001171.6(ABCC6):c.3883-46A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00371 in 1,533,288 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0027 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0038 ( 25 hom. )
Consequence
ABCC6
NM_001171.6 intron
NM_001171.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.16
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 Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS2
?
High Homozygotes in GnomAdExome4 at 25 AD,AR,Digenic gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.3883-46A>G | intron_variant | ENST00000205557.12 | |||
ABCC6 | NM_001351800.1 | c.3541-46A>G | intron_variant | ||||
ABCC6 | NR_147784.1 | n.3545-46A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.3883-46A>G | intron_variant | 1 | NM_001171.6 | P1 | |||
ABCC6 | ENST00000576204.6 | n.700A>G | non_coding_transcript_exon_variant | 1/2 | 5 | ||||
ABCC6 | ENST00000456970.6 | c.*892-46A>G | intron_variant, NMD_transcript_variant | 2 | |||||
ABCC6 | ENST00000622290.5 | c.*55-46A>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00275 AC: 418AN: 152154Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00318 AC: 454AN: 142966Hom.: 2 AF XY: 0.00299 AC XY: 230AN XY: 76826
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GnomAD4 exome AF: 0.00382 AC: 5270AN: 1381016Hom.: 25 Cov.: 31 AF XY: 0.00376 AC XY: 2555AN XY: 679548
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GnomAD4 genome ? AF: 0.00275 AC: 418AN: 152272Hom.: 0 Cov.: 31 AF XY: 0.00267 AC XY: 199AN XY: 74454
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | ABCC6: BS1, BS2 - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at