Genetic Variant SLC11A2:c.-110G>C (chr12-51026381-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_000617.3(SLC11A2):c.-110G>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SLC11A2
NM_000617.3 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.252

Publications

9 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: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, PanelApp Australia, Ambry Genetics, Orphanet, ClinGen, Labcorp Genetics (formerly Invitae)

SLC11A2 links:

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new If you want to explore the variant's impact on the transcript NM_000617.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000617.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC11A2	NM_000617.3	MANE Select	c.-110G>C	5_prime_UTR_premature_start_codon_gain	Exon 1 of 16	NP_000608.1	P49281-2
SLC11A2	NM_000617.3	MANE Select	c.-110G>C	5_prime_UTR	Exon 1 of 16	NP_000608.1	P49281-2
SLC11A2	NM_001174126.2		c.-110G>C	5_prime_UTR_premature_start_codon_gain	Exon 1 of 17	NP_001167597.1	A0A0X8GKR4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC11A2	ENST00000262052.9	TSL:1 MANE Select	c.-110G>C	5_prime_UTR_premature_start_codon_gain	Exon 1 of 16	ENSP00000262052.5	P49281-2
SLC11A2	ENST00000546743.5	TSL:1	c.-267G>C	5_prime_UTR_premature_start_codon_gain	Exon 1 of 16	ENSP00000446914.1	F8W1P7
SLC11A2	ENST00000262052.9	TSL:1 MANE Select	c.-110G>C	5_prime_UTR	Exon 1 of 16	ENSP00000262052.5	P49281-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1126160

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

552644

African (AFR)

AF:

0.00

AC:

AN:

24062

American (AMR)

AF:

0.00

AC:

AN:

28040

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15830

East Asian (EAS)

AF:

0.00

AC:

AN:

12660

South Asian (SAS)

AF:

0.00

AC:

AN:

75728

European-Finnish (FIN)

AF:

0.00

AC:

AN:

12634

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2748

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

913448

Other (OTH)

AF:

0.00

AC:

AN:

41010

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

7.2

(source)

DANN

Benign

0.25

PhyloP100

-0.25

PromoterAI

-0.022

Neutral

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over