rs15897

Variant names:

• chr12-50981140-A-G
• rs15897
• ENST00000547198.5:c.*586T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

SLC11A2 Gene-Disease associations (from GenCC):

• microcytic anemia with liver iron overload

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC11A2	NR_183177.1	n.2642T>C		non_coding_transcript_exon_variant	Exon 17 of 17
SLC11A2	NR_183178.1	n.2647T>C		non_coding_transcript_exon_variant	Exon 17 of 17
SLC11A2	NM_001379446.1	c.*586T>C		3_prime_UTR_variant	Exon 17 of 17		NP_001366375.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC11A2	ENST00000547198.5	c.*586T>C		3_prime_UTR_variant	Exon 17 of 17	1		ENSP00000446769.1
SLC11A2	ENST00000546636.5	n.*87+499T>C		intron_variant	Intron 17 of 17	1		ENSP00000449008.1
SLC11A2	ENST00000547688.7	c.*586T>C		3_prime_UTR_variant	Exon 17 of 17	5		ENSP00000449200.2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0671 AC: 2789 AN: 41540

American (AMR) AF: 0.128 AC: 1950 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 563 AN: 3464

East Asian (EAS) AF: 0.115 AC: 595 AN: 5188

South Asian (SAS) AF: 0.264 AC: 1275 AN: 4822

European-Finnish (FIN) AF: 0.151 AC: 1600 AN: 10578

Middle Eastern (MID) AF: 0.193 AC: 56 AN: 290

European-Non Finnish (NFE) AF: 0.189 AC: 12828 AN: 67988

Other (OTH) AF: 0.165 AC: 348 AN: 2114

Alfa AF: 0.140 Hom.: 266

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
PhyloP100		2.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs15897; hg19: chr12-51374923;