dbSNP rs13062: SLC11A1:n.5673C>A (chr2-218395928-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000468221.5(SLC11A1):n.5673C>A 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 0.365 in 152,356 control chromosomes in the GnomAD database, including 10,278 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 0.36 ( 10265 hom., cov: 33)

Exomes 𝑓: 0.34 ( 13 hom. )

Consequence

SLC11A1
ENST00000468221.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.170

Publications

30 publications found

Variant links:

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

SLC11A1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC11A1	NM_000578.4 link	c.*893C>A		3_prime_UTR_variant	Exon 15 of 15	ENST00000233202.11	NP_000569.3	P49279-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC11A1	ENST00000468221.5 link	n.5673C>A	non_coding_transcript_exon_variant	Exon 13 of 13	1
SLC11A1	ENST00000233202.11 link	c.*893C>A	3_prime_UTR_variant	Exon 15 of 15	1	NM_000578.4	ENSP00000233202.6	P49279-1
SLC11A1	ENST00000465984.5 link	n.2450C>A	non_coding_transcript_exon_variant	Exon 14 of 14	2

Frequencies

GnomAD3 genomes

AF:

0.365

AC:

55438

AN:

151996

Hom.:

10254

Cov.:

show subpopulations

Gnomad AFR

AF:

0.398

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.376

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.363

Gnomad OTH

AF:

0.365

GnomAD4 exome

AF:

0.343

AC:

AN:

242

Hom.:

Cov.:

AF XY:

0.339

AC XY:

AN XY:

168

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.355

AC:

AN:

138

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.284

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.365

AC:

55490

AN:

152114

Hom.:

10265

Cov.:

AF XY:

0.363

AC XY:

26997

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.398

AC:

16507

AN:

41486

American (AMR)

AF:

0.377

AC:

5755

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

1116

AN:

3470

East Asian (EAS)

AF:

0.263

AC:

1365

AN:

5184

South Asian (SAS)

AF:

0.270

AC:

1301

AN:

4822

European-Finnish (FIN)

AF:

0.343

AC:

3632

AN:

10580

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.363

AC:

24706

AN:

67980

Other (OTH)

AF:

0.368

AC:

777

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1823

3645

5468

7290

9113

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

544

1088

1632

2176

2720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.364

Hom.:

11858

Bravo

AF:

0.372

Asia WGS

AF:

0.285

AC:

991

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

3.3

(source)

DANN

Benign

0.80

PhyloP100

-0.17

Mutation Taster

=100/0

polymorphism (auto)

(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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over