2-218395295-A-AAAAC

Position:

• chr2-218395295-A-AAAAC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000578.4(SLC11A1):​c.*269_*272dupAAAC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.36 (10119 hom., cov: 0)
  • Exomes 𝑓: 0.29 (13213 hom.)
• Consequence: SLC11A1 NM_000578.4 3_prime_UTR
• 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]

SLC11A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC11A1	NM_000578.4	c.*269_*272dupAAAC		3_prime_UTR_variant	15/15	ENST00000233202.11	NP_000569.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC11A1	ENST00000233202.11	c.*269_*272dupAAAC		3_prime_UTR_variant	15/15	1	NM_000578.4	ENSP00000233202.6

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55192 AN: 151390 Hom.: 10107 Cov.: 0

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.288 AC: 80452 AN: 279464 Hom.: 13213 Cov.: 0 AF XY: 0.282 AC XY: 40882 AN XY: 145218

Gnomad4 AFR exome AF: 0.339

Gnomad4 AMR exome AF: 0.329

Gnomad4 ASJ exome AF: 0.270

Gnomad4 EAS exome AF: 0.186

Gnomad4 SAS exome AF: 0.225

Gnomad4 FIN exome AF: 0.264

Gnomad4 NFE exome AF: 0.307

Gnomad4 OTH exome AF: 0.304

GnomAD4 genome AF: 0.365 AC: 55244 AN: 151510 Hom.: 10119 Cov.: 0 AF XY: 0.363 AC XY: 26847 AN XY: 74032

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.369

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17229009; hg19: chr2-219260018;