rs13062

Positions:

• chr2-218395928-C-A
• chr2-218395928-C-G
• chr2-218395928-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

ACMG classification

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: 55438 AN: 151996 Hom.: 10254 Cov.: 33

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.365

GnomAD4 exome AF: 0.343 AC: 83 AN: 242 Hom.: 13 Cov.: 0 AF XY: 0.339 AC XY: 57 AN XY: 168

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.355

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.284

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.365 AC: 55490 AN: 152114 Hom.: 10265 Cov.: 33 AF XY: 0.363 AC XY: 26997 AN XY: 74370

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.368

Alfa AF: 0.362 Hom.: 9864

Bravo AF: 0.372

Asia WGS AF: 0.285 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.3
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13062; hg19: chr2-219260651;