rs823154

Variant names:

• chr1-205793278-C-T
• rs823154
• NM_173854.6:c.1357-1560G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173854.6(SLC41A1):​c.1357-1560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,048 control chromosomes in the GnomAD database, including 8,492 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (8492 hom., cov: 32)
• Consequence: SLC41A1 NM_173854.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.15
• 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 Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC41A1	NM_173854.6	MANE Select	c.1357-1560G>A		intron	N/A	NP_776253.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC41A1	ENST00000367137.4	TSL:1 MANE Select	c.1357-1560G>A		intron	N/A	ENSP00000356105.3
	SLC41A1	ENST00000468057.5	TSL:2	n.1153-1560G>A		intron	N/A
	SLC41A1	ENST00000484228.1	TSL:2	n.1423-1560G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47387 AN: 151930 Hom.: 8497 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.333

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.312 AC: 47384 AN: 152048 Hom.: 8492 Cov.: 32 AF XY: 0.306 AC XY: 22729 AN XY: 74314

African (AFR) AF: 0.202 AC: 8381 AN: 41496

American (AMR) AF: 0.274 AC: 4179 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1268 AN: 3468

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5186

South Asian (SAS) AF: 0.147 AC: 709 AN: 4816

European-Finnish (FIN) AF: 0.439 AC: 4624 AN: 10540

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27125 AN: 67956

Other (OTH) AF: 0.329 AC: 693 AN: 2106

Alfa AF: 0.359 Hom.: 28026

Bravo AF: 0.292

Asia WGS AF: 0.0730 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.0050
DANN	Benign	0.37
PhyloP100		-7.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs823154; hg19: chr1-205762406;