rs11240569

Variant names:

• chr1-205810103-G-A
• rs11240569
• NM_173854.6:c.339C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-205810103-G-A
• chr1-205810103-G-C

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_173854.6(SLC41A1):​c.339C>T​(p.Thr113Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 1,614,008 control chromosomes in the GnomAD database, including 70,562 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T113T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.23 (5370 hom., cov: 32)
  • Exomes 𝑓: 0.29 (65192 hom.)
• Consequence: SLC41A1 NM_173854.6 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -1.34
• Publications: 31 publications found

Genes affected

SLC41A1 (HGNC:19429): (solute carrier family 41 member 1) Enables magnesium ion transmembrane transporter activity and magnesium:sodium antiporter activity. Involved in cellular magnesium ion homeostasis; cellular response to magnesium ion; and magnesium ion transmembrane transport. Located in basolateral plasma membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

SLC41A1 Gene-Disease associations (from GenCC):

• kidney disorder

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen
• nephronophthisis-like nephropathy 2

  Inheritance: Unknown, AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia

ACMG classification

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 1-205810103-G-A is Benign according to our data. Variant chr1-205810103-G-A is described in ClinVar as Benign. ClinVar VariationId is 1231809.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-1.34 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173854.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC41A1	NM_173854.6	MANE Select	c.339C>T	p.Thr113Thr	synonymous	Exon 2 of 11	NP_776253.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC41A1	ENST00000367137.4	TSL:1 MANE Select	c.339C>T	p.Thr113Thr	synonymous	Exon 2 of 11	ENSP00000356105.3	Q8IVJ1
	SLC41A1	ENST00000911130.1		c.339C>T	p.Thr113Thr	synonymous	Exon 2 of 11	ENSP00000581189.1
	SLC41A1	ENST00000948596.1		c.339C>T	p.Thr113Thr	synonymous	Exon 2 of 11	ENSP00000618655.1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35427 AN: 152020 Hom.: 5360 Cov.: 32

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.236

GnomAD2 exomes AF: 0.293 AC: 73496 AN: 250936 AF XY: 0.303

Gnomad AFR exome AF: 0.0525

Gnomad AMR exome AF: 0.193

Gnomad ASJ exome AF: 0.300

Gnomad EAS exome AF: 0.577

Gnomad FIN exome AF: 0.282

Gnomad NFE exome AF: 0.292

Gnomad OTH exome AF: 0.294

GnomAD4 exome AF: 0.291 AC: 425315 AN: 1461870 Hom.: 65192 Cov.: 39 AF XY: 0.295 AC XY: 214602 AN XY: 727240

African (AFR) AF: 0.0481 AC: 1609 AN: 33480

American (AMR) AF: 0.196 AC: 8782 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 7780 AN: 26136

East Asian (EAS) AF: 0.550 AC: 21839 AN: 39698

South Asian (SAS) AF: 0.372 AC: 32103 AN: 86256

European-Finnish (FIN) AF: 0.279 AC: 14878 AN: 53418

Middle Eastern (MID) AF: 0.338 AC: 1952 AN: 5768

European-Non Finnish (NFE) AF: 0.287 AC: 318735 AN: 1111996

Other (OTH) AF: 0.292 AC: 17637 AN: 60394

GnomAD4 genome AF: 0.233 AC: 35431 AN: 152138 Hom.: 5370 Cov.: 32 AF XY: 0.238 AC XY: 17717 AN XY: 74384

African (AFR) AF: 0.0572 AC: 2373 AN: 41520

American (AMR) AF: 0.220 AC: 3370 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1036 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2849 AN: 5152

South Asian (SAS) AF: 0.384 AC: 1855 AN: 4826

European-Finnish (FIN) AF: 0.288 AC: 3046 AN: 10580

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.294 AC: 19983 AN: 67978

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.265 Hom.: 3195

Bravo AF: 0.219

Asia WGS AF: 0.440 AC: 1526 AN: 3478

EpiCase AF: 0.292

EpiControl AF: 0.293

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	3	not provided (3)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.2
DANN	Benign	0.76
PhyloP100		-1.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs11240569; hg19: chr1-205779231; COSMIC: COSV65650164; COSMIC: COSV65650164;