16-16150196-C-T
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001171.6(ABCC6):c.4449G>A(p.Pro1483=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
ABCC6
NM_001171.6 synonymous
NM_001171.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.23
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 -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 16-16150196-C-T is Benign according to our data. Variant chr16-16150196-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1640636.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.23 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.4449G>A | p.Pro1483= | synonymous_variant | 31/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.4107G>A | p.Pro1369= | synonymous_variant | 31/31 | ||
ABCC6 | NR_147784.1 | n.4111G>A | non_coding_transcript_exon_variant | 29/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.4449G>A | p.Pro1483= | synonymous_variant | 31/31 | 1 | NM_001171.6 | P1 | |
ABCC6 | ENST00000456970.6 | c.*1458G>A | 3_prime_UTR_variant, NMD_transcript_variant | 29/29 | 2 | ||||
ABCC6 | ENST00000622290.5 | c.*621G>A | 3_prime_UTR_variant, NMD_transcript_variant | 32/32 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248596Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135200
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GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461312Hom.: 0 Cov.: 30 AF XY: 0.0000316 AC XY: 23AN XY: 726970
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_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