rs17229009
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000578.4(SLC11A1):c.*269_*272del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000037 in 432,088 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000040 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000036 ( 0 hom. )
Consequence
SLC11A1
NM_000578.4 3_prime_UTR
NM_000578.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.11
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC11A1 | NM_000578.4 | c.*269_*272del | 3_prime_UTR_variant | 15/15 | ENST00000233202.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC11A1 | ENST00000233202.11 | c.*269_*272del | 3_prime_UTR_variant | 15/15 | 1 | NM_000578.4 | P1 | ||
SLC11A1 | ENST00000468221.5 | n.5049_5052del | non_coding_transcript_exon_variant | 13/13 | 1 | ||||
SLC11A1 | ENST00000354352.9 | c.*1504_*1507del | 3_prime_UTR_variant, NMD_transcript_variant | 16/16 | 1 | ||||
SLC11A1 | ENST00000465984.5 | n.2160+238_2160+241del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000396 AC: 6AN: 151506Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000356 AC: 10AN: 280582Hom.: 0 AF XY: 0.0000412 AC XY: 6AN XY: 145794
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ClinVar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at