rs15897

Positions:

• chr12-50981140-A-G
• chr12-50981140-A-T

Variant summary

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

The ENST00000547198.5(SLC11A2):​c.*586T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,174 control chromosomes in the GnomAD database, including 1,861 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 0.15 (1861 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLC11A2 ENST00000547198.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

Genes affected

SLC11A2 (HGNC:10908): (solute carrier family 11 member 2) This gene encodes a member of the solute carrier family 11 protein family. The product of this gene transports divalent metals and is involved in iron absorption. Mutations in this gene are associated with hypochromic microcytic anemia with iron overload. A related solute carrier family 11 protein gene is located on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC11A2	NM_001174126.2	c.*586T>C		3_prime_UTR_variant	17/17
SLC11A2	NM_001174127.2	c.*586T>C		3_prime_UTR_variant	17/17
SLC11A2	NM_001379446.1	c.*586T>C		3_prime_UTR_variant	17/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC11A2	ENST00000547198.5	c.*586T>C		3_prime_UTR_variant	17/17	1		P1
SLC11A2	ENST00000546636.5	c.*87+499T>C		intron_variant, NMD_transcript_variant		1
SLC11A2	ENST00000547688.7	c.*586T>C		3_prime_UTR_variant	17/17	5

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22168 AN: 152056 Hom.: 1856 Cov.: 32

Gnomad AFR AF: 0.0673

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.166

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.146 AC: 22176 AN: 152174 Hom.: 1861 Cov.: 32 AF XY: 0.146 AC XY: 10848 AN XY: 74388

Gnomad4 AFR AF: 0.0671

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.165

Alfa AF: 0.143 Hom.: 264

Bravo AF: 0.136

Asia WGS AF: 0.158 AC: 546 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs15897; hg19: chr12-51374923;