rs422982

Positions:

• chr12-51012571-T-A
• chr12-51012571-T-C
• chr12-51012571-T-G

Variant summary

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

The NM_000617.3(SLC11A2):​c.-38-1805A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,102 control chromosomes in the GnomAD database, including 37,865 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 0.69 (37865 hom., cov: 31)
• Consequence: SLC11A2 NM_000617.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

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 = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC11A2	NM_000617.3	c.-38-1805A>T		intron_variant		ENST00000262052.9	NP_000608.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC11A2	ENST00000262052.9	c.-38-1805A>T		intron_variant		1	NM_000617.3	ENSP00000262052.5

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105539 AN: 151984 Hom.: 37850 Cov.: 31

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.705

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.694 AC: 105580 AN: 152102 Hom.: 37865 Cov.: 31 AF XY: 0.700 AC XY: 52073 AN XY: 74354

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.708

Alfa AF: 0.657 Hom.: 2176

Bravo AF: 0.687

Asia WGS AF: 0.764 AC: 2658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.44

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

Publications

LitVar

Other links and lift over

dbSNP: rs422982; hg19: chr12-51406354;