rs17229009

Variant names:

• chr2-218395295-AAAAC-A
• rs17229009
• ENST00000354352.9:n.*1504_*1507delAAAC

Your query was ambiguous. Multiple possible variants found:

• chr2-218395295-AAAAC-A
• chr2-218395295-AAAAC-AAAACAAAC
• chr2-218395295-AAAAC-AAAACAAACAAAC

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000354352.9(SLC11A1):​n.*1504_*1507delAAAC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000037 in 432,088 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000040 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000036 (0 hom.)
• Consequence: SLC11A1 ENST00000354352.9 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11
• Publications: 2 publications found

Genes affected

SLC11A1 (HGNC:10907): (solute carrier family 11 member 1) This gene is a member of the solute carrier family 11 (proton-coupled divalent metal ion transporters) family and encodes a multi-pass membrane protein. The protein functions as a divalent transition metal (iron and manganese) transporter involved in iron metabolism and host resistance to certain pathogens. Mutations in this gene have been associated with susceptibility to infectious diseases such as tuberculosis and leprosy, and inflammatory diseases such as rheumatoid arthritis and Crohn disease. Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only one has been determined. [provided by RefSeq, Jul 2008]

SLC11A1 Gene-Disease associations (from GenCC):

• cystic fibrosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000354352.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC11A1	NM_000578.4	MANE Select	c.*269_*272delAAAC		3_prime_UTR	Exon 15 of 15	NP_000569.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC11A1	ENST00000354352.9	TSL:1	n.*1504_*1507delAAAC		non_coding_transcript_exon	Exon 16 of 16	ENSP00000346320.5
	SLC11A1	ENST00000468221.5	TSL:1	n.5049_5052delAAAC		non_coding_transcript_exon	Exon 13 of 13
	SLC11A1	ENST00000233202.11	TSL:1 MANE Select	c.*269_*272delAAAC		3_prime_UTR	Exon 15 of 15	ENSP00000233202.6

Frequencies

GnomAD3 genomes AF: 0.0000396 AC: 6 AN: 151506 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000485

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000658

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000443

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000356 AC: 10 AN: 280582 Hom.: 0 AF XY: 0.0000412 AC XY: 6 AN XY: 145794

African (AFR) AF: 0.00 AC: 0 AN: 8852

American (AMR) AF: 0.00 AC: 0 AN: 10398

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9224

East Asian (EAS) AF: 0.00 AC: 0 AN: 21240

South Asian (SAS) AF: 0.00 AC: 0 AN: 25204

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 18116

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1340

European-Non Finnish (NFE) AF: 0.0000591 AC: 10 AN: 169302

Other (OTH) AF: 0.00 AC: 0 AN: 16906

GnomAD4 genome AF: 0.0000396 AC: 6 AN: 151506 Hom.: 0 Cov.: 0 AF XY: 0.0000541 AC XY: 4 AN XY: 73970

African (AFR) AF: 0.0000485 AC: 2 AN: 41214

American (AMR) AF: 0.0000658 AC: 1 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10542

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.0000443 AC: 3 AN: 67794

Other (OTH) AF: 0.00 AC: 0 AN: 2082

Alfa AF: 0.0000879 Hom.: 221

Bravo AF: 0.0000416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17229009; hg19: chr2-219260018;