Variant chr1-205795512-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_173854.6(SLC41A1):c.1073-34C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 1,612,772 control chromosomes in the GnomAD database, including 517,217 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 40181 hom., cov: 32)

Exomes 𝑓: 0.80 ( 477036 hom. )

Consequence

SLC41A1
NM_173854.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.24

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 1-205795512-G-A is Benign according to our data. Variant chr1-205795512-G-A is described in ClinVar as [Benign]. Clinvar id is 1183197.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A1	NM_173854.6 linkuse as main transcript	c.1073-34C>T		intron_variant		ENST00000367137.4
SLC41A1	XM_047416887.1 linkuse as main transcript	c.1073-34C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
SLC41A1	ENST00000367137.4 linkuse as main transcript	c.1073-34C>T	intron_variant		1	NM_173854.6	P1
SLC41A1	ENST00000484228.1 linkuse as main transcript	n.1105C>T	non_coding_transcript_exon_variant	1/3	2
SLC41A1	ENST00000468057.5 linkuse as main transcript	n.869-34C>T	intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.704

AC:

107067

AN:

152014

Hom.:

40164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.421

Gnomad AMI

AF:

0.914

Gnomad AMR

AF:

0.761

Gnomad ASJ

AF:

0.776

Gnomad EAS

AF:

0.792

Gnomad SAS

AF:

0.744

Gnomad FIN

AF:

0.833

Gnomad MID

AF:

0.736

Gnomad NFE

AF:

0.827

Gnomad OTH

AF:

0.724

GnomAD3 exomes

AF:

0.772

AC:

192566

AN:

249422

Hom.:

75638

AF XY:

0.778

AC XY:

104948

AN XY:

134874

show subpopulations

Gnomad AFR exome

AF:

0.409

Gnomad AMR exome

AF:

0.743

Gnomad ASJ exome

AF:

0.794

Gnomad EAS exome

AF:

0.801

Gnomad SAS exome

AF:

0.740

Gnomad FIN exome

AF:

0.826

Gnomad NFE exome

AF:

0.824

Gnomad OTH exome

AF:

0.780

GnomAD4 exome

AF:

0.805

AC:

1175736

AN:

1460640

Hom.:

477036

Cov.:

AF XY:

0.804

AC XY:

584429

AN XY:

726648

show subpopulations

Gnomad4 AFR exome

AF:

0.400

Gnomad4 AMR exome

AF:

0.745

Gnomad4 ASJ exome

AF:

0.793

Gnomad4 EAS exome

AF:

0.820

Gnomad4 SAS exome

AF:

0.742

Gnomad4 FIN exome

AF:

0.828

Gnomad4 NFE exome

AF:

0.825

Gnomad4 OTH exome

AF:

0.779

GnomAD4 genome

AF:

0.704

AC:

107128

AN:

152132

Hom.:

40181

Cov.:

AF XY:

0.706

AC XY:

52511

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.421

Gnomad4 AMR

AF:

0.761

Gnomad4 ASJ

AF:

0.776

Gnomad4 EAS

AF:

0.792

Gnomad4 SAS

AF:

0.745

Gnomad4 FIN

AF:

0.833

Gnomad4 NFE

AF:

0.827

Gnomad4 OTH

AF:

0.727

Alfa

AF:

0.803

Hom.:

114909

Bravo

AF:

0.685

Asia WGS

AF:

0.746

AC:

2594

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.46

DANN

Benign

0.46

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