NM_001352171.3:c.1175+41_1175+50delGTGTGTGTGT

Variant names:

• chr12-104866381-TACACACACAC-T
• rs57548373
• NM_001352171.3:c.1175+41_1175+50delGTGTGTGTGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001352171.3(SLC41A2):​c.1175+41_1175+50delGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00643 in 1,419,900 control chromosomes in the GnomAD database, including 71 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.018 (56 hom., cov: 0)
  • Exomes 𝑓: 0.0052 (15 hom.)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94

Genes affected

SLC41A2 (HGNC:31045): (solute carrier family 41 member 2) Predicted to enable inorganic cation transmembrane transporter activity. Predicted to be involved in magnesium ion transmembrane transport. Predicted to act upstream of or within metal ion transport. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000286410 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3	c.1175+41_1175+50delGTGTGTGTGT		intron_variant	Intron 7 of 10	ENST00000258538.8	NP_001339100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1175+41_1175+50delGTGTGTGTGT		intron_variant	Intron 7 of 10	1	NM_001352171.3	ENSP00000258538.3
ENSG00000286410	ENST00000671114.1	n.71-3780_71-3771delACACACACAC		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0179 AC: 2520 AN: 140992 Hom.: 56 Cov.: 0

Gnomad AFR AF: 0.0570

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0122

Gnomad ASJ AF: 0.000601

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00284

Gnomad FIN AF: 0.00197

Gnomad MID AF: 0.00342

Gnomad NFE AF: 0.00283

Gnomad OTH AF: 0.0181

GnomAD3 exomes AF: 0.0132 AC: 1992 AN: 151248 Hom.: 26 AF XY: 0.0119 AC XY: 981 AN XY: 82436

Gnomad AFR exome AF: 0.0681

Gnomad AMR exome AF: 0.0135

Gnomad ASJ exome AF: 0.00691

Gnomad EAS exome AF: 0.0197

Gnomad SAS exome AF: 0.00746

Gnomad FIN exome AF: 0.00516

Gnomad NFE exome AF: 0.00719

Gnomad OTH exome AF: 0.00963

GnomAD4 exome AF: 0.00516 AC: 6604 AN: 1278816 Hom.: 15 AF XY: 0.00515 AC XY: 3236 AN XY: 628368

Gnomad4 AFR exome AF: 0.0556

Gnomad4 AMR exome AF: 0.0121

Gnomad4 ASJ exome AF: 0.00465

Gnomad4 EAS exome AF: 0.0105

Gnomad4 SAS exome AF: 0.00558

Gnomad4 FIN exome AF: 0.00399

Gnomad4 NFE exome AF: 0.00321

Gnomad4 OTH exome AF: 0.00760

GnomAD4 genome AF: 0.0179 AC: 2525 AN: 141084 Hom.: 56 Cov.: 0 AF XY: 0.0175 AC XY: 1203 AN XY: 68658

Gnomad4 AFR AF: 0.0570

Gnomad4 AMR AF: 0.0121

Gnomad4 ASJ AF: 0.000601

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00284

Gnomad4 FIN AF: 0.00197

Gnomad4 NFE AF: 0.00283

Gnomad4 OTH AF: 0.0180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs57548373; hg19: chr12-105260159;