rs706804

Positions:

• chr12-50981283-G-A
• chr12-50981283-G-C
• chr12-50981283-G-T

Variant summary

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

The NM_001379446.1(SLC11A2):​c.*443C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,930 control chromosomes in the GnomAD database, including 60,119 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 0.88 (59793 hom., cov: 31)
  • Exomes 𝑓: 0.95 (326 hom.)
• Consequence: SLC11A2 NM_001379446.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC11A2	NM_001379446.1	c.*443C>T		3_prime_UTR_variant	17/17		NP_001366375.1
SLC11A2	NM_001174126.2	c.*443C>T		3_prime_UTR_variant	17/17		NP_001167597.1
SLC11A2	NM_001174127.2	c.*443C>T		3_prime_UTR_variant	17/17		NP_001167598.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC11A2	ENST00000547198	c.*443C>T		3_prime_UTR_variant	17/17	1		ENSP00000446769.1
SLC11A2	ENST00000546636.5	n.*87+356C>T		intron_variant		1		ENSP00000449008.1
SLC11A2	ENST00000547688	c.*443C>T		3_prime_UTR_variant	17/17	5		ENSP00000449200.2

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133866 AN: 152092 Hom.: 59732 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.901

GnomAD4 exome AF: 0.950 AC: 684 AN: 720 Hom.: 326 Cov.: 0 AF XY: 0.958 AC XY: 299 AN XY: 312

Gnomad4 AFR exome AF: 0.625

Gnomad4 AMR exome AF: 0.967

Gnomad4 ASJ exome AF: 0.667

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.962

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.953

Gnomad4 OTH exome AF: 0.893

GnomAD4 genome AF: 0.880 AC: 133982 AN: 152210 Hom.: 59793 Cov.: 31 AF XY: 0.885 AC XY: 65897 AN XY: 74428

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.982

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.902

Alfa AF: 0.904 Hom.: 8695

Bravo AF: 0.868

Asia WGS AF: 0.938 AC: 3260 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs706804; hg19: chr12-51375066;