rs13062
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000578.4(SLC11A1):c.*893C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,356 control chromosomes in the GnomAD database, including 10,278 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 0.36 ( 10265 hom., cov: 33)
Exomes 𝑓: 0.34 ( 13 hom. )
Consequence
SLC11A1
NM_000578.4 3_prime_UTR
NM_000578.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.170
Genes affected
SLC11A1 (HGNC:10907): (solute carrier family 11 member 1) This gene is a member of the solute carrier family 11 (proton-coupled divalent metal ion transporters) family and encodes a multi-pass membrane protein. The protein functions as a divalent transition metal (iron and manganese) transporter involved in iron metabolism and host resistance to certain pathogens. Mutations in this gene have been associated with susceptibility to infectious diseases such as tuberculosis and leprosy, and inflammatory diseases such as rheumatoid arthritis and Crohn disease. Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only one has been determined. [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=-0.7).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC11A1 | NM_000578.4 | c.*893C>A | 3_prime_UTR_variant | 15/15 | ENST00000233202.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC11A1 | ENST00000233202.11 | c.*893C>A | 3_prime_UTR_variant | 15/15 | 1 | NM_000578.4 | P1 | ||
SLC11A1 | ENST00000468221.5 | n.5673C>A | non_coding_transcript_exon_variant | 13/13 | 1 | ||||
SLC11A1 | ENST00000465984.5 | n.2450C>A | non_coding_transcript_exon_variant | 14/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.365 AC: 55438AN: 151996Hom.: 10254 Cov.: 33
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GnomAD4 exome AF: 0.343 AC: 83AN: 242Hom.: 13 Cov.: 0 AF XY: 0.339 AC XY: 57AN XY: 168
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GnomAD4 genome ? AF: 0.365 AC: 55490AN: 152114Hom.: 10265 Cov.: 33 AF XY: 0.363 AC XY: 26997AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
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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