Variant rs708727 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.756C>T(p.Asn252=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 1,613,886 control chromosomes in the GnomAD database, including 117,190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 8147 hom., cov: 32)

Exomes 𝑓: 0.37 ( 109043 hom. )

Consequence

SLC41A1
NM_173854.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.410

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=-0.47).

BP6

Variant 1-205798757-G-A is Benign according to our data. Variant chr1-205798757-G-A is described in ClinVar as [Benign]. Clinvar id is 1553777.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.41 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 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.756C>T	p.Asn252=	synonymous_variant	6/11	ENST00000367137.4	NP_776253.3
SLC41A1	XM_047416887.1 linkuse as main transcript	c.756C>T	p.Asn252=	synonymous_variant	5/10		XP_047272843.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC41A1	ENST00000367137.4 linkuse as main transcript	c.756C>T	p.Asn252=	synonymous_variant	6/11	1	NM_173854.6	ENSP00000356105	P1
SLC41A1	ENST00000468057.5 linkuse as main transcript	n.552C>T		non_coding_transcript_exon_variant	5/10	2

Frequencies

GnomAD3 genomes

AF:

0.284

AC:

43100

AN:

151892

Hom.:

8152

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0768

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.368

Gnomad EAS

AF:

0.00310

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.445

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.413

Gnomad OTH

AF:

0.316

GnomAD3 exomes

AF:

0.296

AC:

74486

AN:

251468

Hom.:

14155

AF XY:

0.301

AC XY:

40856

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.0653

Gnomad AMR exome

AF:

0.181

Gnomad ASJ exome

AF:

0.372

Gnomad EAS exome

AF:

0.000870

Gnomad SAS exome

AF:

0.155

Gnomad FIN exome

AF:

0.442

Gnomad NFE exome

AF:

0.414

Gnomad OTH exome

AF:

0.336

GnomAD4 exome

AF:

0.370

AC:

540921

AN:

1461876

Hom.:

109043

Cov.:

AF XY:

0.365

AC XY:

265123

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.0606

Gnomad4 AMR exome

AF:

0.189

Gnomad4 ASJ exome

AF:

0.376

Gnomad4 EAS exome

AF:

0.000831

Gnomad4 SAS exome

AF:

0.158

Gnomad4 FIN exome

AF:

0.444

Gnomad4 NFE exome

AF:

0.415

Gnomad4 OTH exome

AF:

0.337

GnomAD4 genome

AF:

0.283

AC:

43085

AN:

152010

Hom.:

8147

Cov.:

AF XY:

0.279

AC XY:

20711

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.0766

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.368

Gnomad4 EAS

AF:

0.00310

Gnomad4 SAS

AF:

0.150

Gnomad4 FIN

AF:

0.445

Gnomad4 NFE

AF:

0.413

Gnomad4 OTH

AF:

0.312

Alfa

AF:

0.378

Hom.:

20125

Bravo

AF:

0.260

Asia WGS

AF:

0.0690

AC:

244

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 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

-0.47

CADD

Benign

3.1

DANN

Benign

0.80

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over