rs2018673

Positions:

• chr12-50992747-G-A

Variant summary

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

The NM_000617.3(SLC11A2):​c.1197+63C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.54 (19999 hom., cov: 17)
  • Exomes 𝑓: 0.45 (44083 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC11A2 NM_000617.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC11A2	NM_000617.3	c.1197+63C>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.1197+63C>T		intron_variant		1	NM_000617.3	ENSP00000262052.5

Frequencies

GnomAD3 genomes AF: 0.542 AC: 68151 AN: 125770 Hom.: 19995 Cov.: 17

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.467

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.549

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.448 AC: 356742 AN: 797078 Hom.: 44083 AF XY: 0.453 AC XY: 180524 AN XY: 398770

Gnomad4 AFR exome AF: 0.432

Gnomad4 AMR exome AF: 0.563

Gnomad4 ASJ exome AF: 0.476

Gnomad4 EAS exome AF: 0.351

Gnomad4 SAS exome AF: 0.456

Gnomad4 FIN exome AF: 0.533

Gnomad4 NFE exome AF: 0.443

Gnomad4 OTH exome AF: 0.455

GnomAD4 genome AF: 0.542 AC: 68150 AN: 125768 Hom.: 19999 Cov.: 17 AF XY: 0.529 AC XY: 31103 AN XY: 58814

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.548

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.51

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: rs2018673; hg19: chr12-51386530; COSMIC: COSV50370282; COSMIC: COSV50370282;