rs823154

chr1-205793278-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A1	NM_173854.6	c.1357-1560G>A		intron_variant		ENST00000367137.4
SLC41A1	XM_047416887.1	c.1357-1560G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A1	ENST00000367137.4	c.1357-1560G>A		intron_variant		1	NM_173854.6	P1
SLC41A1	ENST00000468057.5	n.1153-1560G>A		intron_variant, non_coding_transcript_variant		2
SLC41A1	ENST00000484228.1	n.1423-1560G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.329

Alfa AF: 0.373 Hom.: 18487

Bravo AF: 0.292

Asia WGS AF: 0.0730 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.0050
Dann	Benign	0.37

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: rs823154; hg19: chr1-205762406;