12-104866381-TACACACAC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001352171.3(SLC41A2):c.1175+43_1175+50del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,112,090 control chromosomes in the GnomAD database, including 97 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.029 (107 hom., cov: 0)
  • Exomes 𝑓: 0.11 (97 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-104866381-TACACACAC-T is Benign according to our data. Variant chr12-104866381-TACACACAC-T is described in ClinVar as [Benign]. Clinvar id is 1259817.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1175+43_1175+50del		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1175+43_1175+50del		intron_variant		1	NM_001352171.3	P1
	ENST00000671114.1	n.71-3753_71-3746del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0289 AC: 4064 AN: 140624 Hom.: 106 Cov.: 0

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.0116

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.00952

Gnomad MID AF: 0.0483

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0353

GnomAD3 exomes AF: 0.155 AC: 23397 AN: 151248 Hom.: 67 AF XY: 0.156 AC XY: 12849 AN XY: 82436

Gnomad AFR exome AF: 0.131

Gnomad AMR exome AF: 0.166

Gnomad ASJ exome AF: 0.186

Gnomad EAS exome AF: 0.201

Gnomad SAS exome AF: 0.0959

Gnomad FIN exome AF: 0.121

Gnomad NFE exome AF: 0.163

Gnomad OTH exome AF: 0.155

GnomAD4 exome AF: 0.106 AC: 118319 AN: 1112090 Hom.: 97 AF XY: 0.108 AC XY: 59119 AN XY: 548570

Gnomad4 AFR exome AF: 0.0977

Gnomad4 AMR exome AF: 0.161

Gnomad4 ASJ exome AF: 0.158

Gnomad4 EAS exome AF: 0.188

Gnomad4 SAS exome AF: 0.0773

Gnomad4 FIN exome AF: 0.103

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.114

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0289 AC: 4069 AN: 140712 Hom.: 107 Cov.: 0 AF XY: 0.0296 AC XY: 2024 AN XY: 68444

Gnomad4 AFR AF: 0.0503

Gnomad4 AMR AF: 0.0259

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.0159

Gnomad4 FIN AF: 0.00952

Gnomad4 NFE AF: 0.0123

Gnomad4 OTH AF: 0.0371

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 19, 2021

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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;