1-205795512-G-A

Position:

• chr1-205795512-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.24

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]

ACMG classification

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	Protein	UniProt
SLC41A1	NM_173854.6	c.1073-34C>T		intron_variant		ENST00000367137.4	NP_776253.3
SLC41A1	XM_047416887.1	c.1073-34C>T		intron_variant			XP_047272843.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC41A1	ENST00000367137.4	c.1073-34C>T		intron_variant		1	NM_173854.6	ENSP00000356105	P1
SLC41A1	ENST00000484228.1	n.1105C>T		non_coding_transcript_exon_variant	1/3	2
SLC41A1	ENST00000468057.5	n.869-34C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.704 AC: 107067 AN: 152014 Hom.: 40164 Cov.: 32

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

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.: 46 AF XY: 0.804 AC XY: 584429 AN XY: 726648

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.: 32 AF XY: 0.706 AC XY: 52511 AN XY: 74386

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

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

Other links and lift over

dbSNP: rs823156; hg19: chr1-205764640; COSMIC: COSV65650550;