Variant rs11240569 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

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 (★★).

Frequency

Genomes: 𝑓 0.23 ( 5370 hom., cov: 32)

Exomes 𝑓: 0.29 ( 65192 hom. )

Consequence

SLC41A1
NM_173854.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.34

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC41A1	NM_173854.6 linkuse as main transcript	c.339C>T	p.Thr113Thr	synonymous_variant	2/11	ENST00000367137.4	NP_776253.3	Q8IVJ1B2RMP2
SLC41A1	XM_047416887.1 linkuse as main transcript	c.339C>T	p.Thr113Thr	synonymous_variant	1/10		XP_047272843.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC41A1	ENST00000367137.4 linkuse as main transcript	c.339C>T	p.Thr113Thr	synonymous_variant	2/11	1	NM_173854.6	ENSP00000356105.3		Q8IVJ1

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35427

AN:

152020

Hom.:

5360

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.293

AC:

73496

AN:

250936

Hom.:

12343

AF XY:

0.303

AC XY:

41053

AN XY:

135648

show subpopulations

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 SAS exome

AF:

0.371

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.:

AF XY:

0.295

AC XY:

214602

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.0481

Gnomad4 AMR exome

AF:

0.196

Gnomad4 ASJ exome

AF:

0.298

Gnomad4 EAS exome

AF:

0.550

Gnomad4 SAS exome

AF:

0.372

Gnomad4 FIN exome

AF:

0.279

Gnomad4 NFE exome

AF:

0.287

Gnomad4 OTH exome

AF:

0.292

GnomAD4 genome

AF:

0.233

AC:

35431

AN:

152138

Hom.:

5370

Cov.:

AF XY:

0.238

AC XY:

17717

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.0572

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.299

Gnomad4 EAS

AF:

0.553

Gnomad4 SAS

AF:

0.384

Gnomad4 FIN

AF:

0.288

Gnomad4 NFE

AF:

0.294

Gnomad4 OTH

AF:

0.244

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

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

5.2

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over