rs2066738
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001171.6(ABCC6):c.4042-30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,607,040 control chromosomes in the GnomAD database, including 29,556 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2198 hom., cov: 31)
Exomes 𝑓: 0.19 ( 27358 hom. )
Consequence
ABCC6
NM_001171.6 intron
NM_001171.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.51
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 16-16154824-G-A is Benign according to our data. Variant chr16-16154824-G-A is described in ClinVar as [Benign]. Clinvar id is 1258776.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr16-16154824-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.4042-30C>T | intron_variant | ENST00000205557.12 | |||
ABCC6 | NM_001351800.1 | c.3700-30C>T | intron_variant | ||||
ABCC6 | NR_147784.1 | n.3704-30C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.4042-30C>T | intron_variant | 1 | NM_001171.6 | P1 | |||
ABCC6 | ENST00000456970.6 | c.*1051-30C>T | intron_variant, NMD_transcript_variant | 2 | |||||
ABCC6 | ENST00000622290.5 | c.*214-30C>T | intron_variant, NMD_transcript_variant | 5 | |||||
ABCC6 | ENST00000576204.6 | n.905-30C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.156 AC: 23642AN: 151918Hom.: 2201 Cov.: 31
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GnomAD3 exomes AF: 0.209 AC: 49223AN: 235266Hom.: 5720 AF XY: 0.212 AC XY: 27150AN XY: 127788
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GnomAD4 exome AF: 0.188 AC: 273075AN: 1455004Hom.: 27358 Cov.: 33 AF XY: 0.191 AC XY: 137991AN XY: 723296
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GnomAD4 genome ? AF: 0.156 AC: 23645AN: 152036Hom.: 2198 Cov.: 31 AF XY: 0.162 AC XY: 12027AN XY: 74290
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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 | GeneDx | Mar 03, 2015 | - - |
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