1-205798905-C-T

Position:

• chr1-205798905-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_173854.6(SLC41A1):​c.697+52G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00486 in 1,614,128 control chromosomes in the GnomAD database, including 31 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 0.0032 (4 hom., cov: 32)
  • Exomes 𝑓: 0.0050 (27 hom.)
• Consequence: SLC41A1 NM_173854.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC41A1	NM_173854.6	c.697+52G>A		intron_variant		ENST00000367137.4	NP_776253.3
SLC41A1	XM_047416887.1	c.697+52G>A		intron_variant			XP_047272843.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC41A1	ENST00000367137.4	c.697+52G>A		intron_variant		1	NM_173854.6	ENSP00000356105.3
SLC41A1	ENST00000468057.5	n.493+52G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00315 AC: 480 AN: 152186 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.00121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00451

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00492

Gnomad OTH AF: 0.00239

GnomAD4 exome AF: 0.00504 AC: 7367 AN: 1461824 Hom.: 27 Cov.: 34 AF XY: 0.00484 AC XY: 3518 AN XY: 727222

Gnomad4 AFR exome AF: 0.000747

Gnomad4 AMR exome AF: 0.00300

Gnomad4 ASJ exome AF: 0.00341

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00107

Gnomad4 NFE exome AF: 0.00608

Gnomad4 OTH exome AF: 0.00487

GnomAD4 genome AF: 0.00315 AC: 480 AN: 152304 Hom.: 4 Cov.: 32 AF XY: 0.00279 AC XY: 208 AN XY: 74468

Gnomad4 AFR AF: 0.00120

Gnomad4 AMR AF: 0.00451

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00493

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.00149 Hom.: 0

Bravo AF: 0.00368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.66
DANN	Benign	0.38

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: rs41264905; hg19: chr1-205768033;