Genetic Variant SLC11A2:c.*443C>T (chr12-50981283-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000547198.5(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
ENST00000547198.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0950

Publications

4 publications found

Variant links:

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

SLC11A2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	Protein
SLC11A2	NR_183177.1 link	n.2499C>T	non_coding_transcript_exon_variant	Exon 17 of 17
SLC11A2	NR_183178.1 link	n.2504C>T	non_coding_transcript_exon_variant	Exon 17 of 17
SLC11A2	NM_001379446.1 link	c.*443C>T	3_prime_UTR_variant	Exon 17 of 17	NP_001366375.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
SLC11A2	ENST00000547198.5 link	c.*443C>T	3_prime_UTR_variant	Exon 17 of 17	1	ENSP00000446769.1	P49281-1
SLC11A2	ENST00000546636.5 link	n.*87+356C>T	intron_variant	Intron 17 of 17	1	ENSP00000449008.1	P49281-1
SLC11A2	ENST00000547688.7 link	c.*443C>T	3_prime_UTR_variant	Exon 17 of 17	5	ENSP00000449200.2	P49281-4

Frequencies

GnomAD3 genomes

AF:

0.880

AC:

133866

AN:

152092

Hom.:

59732

Cov.:

show subpopulations

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.:

AF XY:

0.958

AC XY:

299

AN XY:

312

show subpopulations

African (AFR)

AF:

0.625

AC:

AN:

American (AMR)

AF:

0.967

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.962

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.953

AC:

471

AN:

494

Other (OTH)

AF:

0.893

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.880

AC:

133982

AN:

152210

Hom.:

59793

Cov.:

AF XY:

0.885

AC XY:

65897

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.713

AC:

29565

AN:

41460

American (AMR)

AF:

0.931

AC:

14237

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.938

AC:

3258

AN:

3472

East Asian (EAS)

AF:

0.983

AC:

5105

AN:

5192

South Asian (SAS)

AF:

0.906

AC:

4375

AN:

4830

European-Finnish (FIN)

AF:

0.982

AC:

10422

AN:

10610

Middle Eastern (MID)

AF:

0.898

AC:

264

AN:

294

European-Non Finnish (NFE)

AF:

0.941

AC:

64012

AN:

68032

Other (OTH)

AF:

0.902

AC:

1905

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

728

1456

2183

2911

3639

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.897

Hom.:

8907

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

(source)

DANN

Benign

0.42

PhyloP100

-0.095

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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chr12-50981283-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over