rs72664294
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001171.6(ABCC6):c.662+403T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0354 in 152,222 control chromosomes in the GnomAD database, including 115 homozygotes. 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 0.035 ( 115 hom., cov: 30)
Consequence
ABCC6
NM_001171.6 intron
NM_001171.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.291
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0354 (5388/152222) while in subpopulation AFR AF= 0.0461 (1915/41510). AF 95% confidence interval is 0.0444. There are 115 homozygotes in gnomad4. There are 2521 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 112 AD,AR,Digenic gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.662+403T>C | intron_variant | ENST00000205557.12 | |||
LOC105371100 | XR_933131.3 | n.89-116A>G | intron_variant, non_coding_transcript_variant | ||||
ABCC6 | NM_001351800.1 | c.320+403T>C | intron_variant | ||||
ABCC6 | NR_147784.1 | n.699+403T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.662+403T>C | intron_variant | 1 | NM_001171.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0353 AC: 5374AN: 152104Hom.: 112 Cov.: 30
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GnomAD4 genome ? AF: 0.0354 AC: 5388AN: 152222Hom.: 115 Cov.: 30 AF XY: 0.0339 AC XY: 2521AN XY: 74416
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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