chr12-50992765-A-G

Position:

• chr12-50992765-A-G

Variant summary

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

The ENST00000262052.9(SLC11A2):​c.1197+45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,595,918 control chromosomes in the GnomAD database, including 24,361 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 0.15 (2208 hom., cov: 28)
  • Exomes 𝑓: 0.16 (22153 hom.)
• Consequence: SLC11A2 ENST00000262052.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC11A2	NM_000617.3	c.1197+45T>C		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+45T>C		intron_variant		1	NM_000617.3	ENSP00000262052

Frequencies

GnomAD3 genomes AF: 0.152 AC: 22924 AN: 150484 Hom.: 2209 Cov.: 28

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.150

GnomAD3 exomes AF: 0.175 AC: 42220 AN: 240628 Hom.: 4930 AF XY: 0.179 AC XY: 23287 AN XY: 130082

Gnomad AFR exome AF: 0.0835

Gnomad AMR exome AF: 0.138

Gnomad ASJ exome AF: 0.189

Gnomad EAS exome AF: 0.455

Gnomad SAS exome AF: 0.221

Gnomad FIN exome AF: 0.167

Gnomad NFE exome AF: 0.146

Gnomad OTH exome AF: 0.152

GnomAD4 exome AF: 0.164 AC: 237392 AN: 1445328 Hom.: 22153 Cov.: 28 AF XY: 0.167 AC XY: 120101 AN XY: 719544

Gnomad4 AFR exome AF: 0.0814

Gnomad4 AMR exome AF: 0.149

Gnomad4 ASJ exome AF: 0.199

Gnomad4 EAS exome AF: 0.445

Gnomad4 SAS exome AF: 0.234

Gnomad4 FIN exome AF: 0.181

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.171

GnomAD4 genome AF: 0.152 AC: 22930 AN: 150590 Hom.: 2208 Cov.: 28 AF XY: 0.157 AC XY: 11502 AN XY: 73330

Gnomad4 AFR AF: 0.0843

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.150

Alfa AF: 0.144 Hom.: 415

Bravo AF: 0.148

Asia WGS AF: 0.320 AC: 1114 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.63

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: rs224568; hg19: chr12-51386548; COSMIC: COSV50369700; COSMIC: COSV50369700;