rs7851395
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001859.4(SLC31A1):c.-35-15930A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,934 control chromosomes in the GnomAD database, including 17,161 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 0.47 ( 17161 hom., cov: 32)
Consequence
SLC31A1
NM_001859.4 intron
NM_001859.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.164
Genes affected
SLC31A1 (HGNC:11016): (solute carrier family 31 member 1) The protein encoded by this gene is a high-affinity copper transporter found in the cell membrane. The encoded protein functions as a homotrimer to effect the uptake of dietary copper. [provided by RefSeq, Aug 2011]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC31A1 | NM_001859.4 | c.-35-15930A>G | intron_variant | ENST00000374212.5 | |||
LOC107987119 | XR_007061737.1 | n.1840T>C | non_coding_transcript_exon_variant | 3/3 | |||
LOC107987119 | XR_007061736.1 | n.1965T>C | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC31A1 | ENST00000374212.5 | c.-35-15930A>G | intron_variant | 1 | NM_001859.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.471 AC: 71454AN: 151816Hom.: 17145 Cov.: 32
GnomAD3 genomes
?
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.471 AC: 71524AN: 151934Hom.: 17161 Cov.: 32 AF XY: 0.475 AC XY: 35262AN XY: 74272
GnomAD4 genome
?
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71524
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151934
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32
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35262
AN XY:
74272
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1958
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3474
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