chr2-218382988-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000578.4(SLC11A1):c.36G>A(p.Gly12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000278 in 1,614,086 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 0.00020 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00029 ( 0 hom. )
Consequence
SLC11A1
NM_000578.4 synonymous
NM_000578.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.382
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 2-218382988-G-A is Benign according to our data. Variant chr2-218382988-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3025428.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.382 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC11A1 | NM_000578.4 | c.36G>A | p.Gly12= | synonymous_variant | 2/15 | ENST00000233202.11 | NP_000569.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC11A1 | ENST00000233202.11 | c.36G>A | p.Gly12= | synonymous_variant | 2/15 | 1 | NM_000578.4 | ENSP00000233202 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152090Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000141 AC: 35AN: 248902Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 134742
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GnomAD4 exome AF: 0.000287 AC: 419AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.000267 AC XY: 194AN XY: 727240
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GnomAD4 genome AF: 0.000197 AC: 30AN: 152208Hom.: 0 Cov.: 31 AF XY: 0.000242 AC XY: 18AN XY: 74408
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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 | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | SLC11A1: BP4, BP7 - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at