Variant rs17235416 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000578.4(SLC11A1):c.*56_*59delTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0355 in 1,370,208 control chromosomes in the GnomAD database, including 2,602 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.082 ( 1034 hom., cov: 32)

Exomes 𝑓: 0.030 ( 1568 hom. )

Consequence

SLC11A1
NM_000578.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.383

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC11A1	NM_000578.4 link	c.56_59delTGTG		3_prime_UTR_variant	15/15	ENST00000233202.11	NP_000569.3	P49279-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC11A1	ENST00000233202.11 link	c.56_59delTGTG		3_prime_UTR_variant	15/15	1	NM_000578.4	ENSP00000233202.6		P49279-1

Frequencies

GnomAD3 genomes

AF:

0.0820

AC:

12444

AN:

151782

Hom.:

1036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0774

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.0667

Gnomad FIN

AF:

0.0226

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0160

Gnomad OTH

AF:

0.0728

GnomAD4 exome

AF:

0.0297

AC:

36147

AN:

1218308

Hom.:

1568

AF XY:

0.0295

AC XY:

17984

AN XY:

609504

show subpopulations

Gnomad4 AFR exome

AF:

0.218

Gnomad4 AMR exome

AF:

0.108

Gnomad4 ASJ exome

AF:

0.0124

Gnomad4 EAS exome

AF:

0.116

Gnomad4 SAS exome

AF:

0.0544

Gnomad4 FIN exome

AF:

0.0196

Gnomad4 NFE exome

AF:

0.0155

Gnomad4 OTH exome

AF:

0.0442

GnomAD4 genome

AF:

0.0820

AC:

12456

AN:

151900

Hom.:

1034

Cov.:

AF XY:

0.0825

AC XY:

6126

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.210

Gnomad4 AMR

AF:

0.0773

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.145

Gnomad4 SAS

AF:

0.0659

Gnomad4 FIN

AF:

0.0226

Gnomad4 NFE

AF:

0.0160

Gnomad4 OTH

AF:

0.0720

Alfa

AF:

0.0525

Hom.:

Bravo

AF:

0.0930

Asia WGS

AF:

0.116

AC:

405

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over