12-104866380-GTACA-G

Variant summary

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

The NM_001352171.3(SLC41A2):c.1175+48_1175+51del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 1,379,602 control chromosomes in the GnomAD database, including 334 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.063 (165 hom., cov: 0)
  • Exomes 𝑓: 0.032 (169 hom.)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.25

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 12-104866380-GTACA-G is Benign according to our data. Variant chr12-104866380-GTACA-G is described in ClinVar as [Benign]. Clinvar id is 1222767.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1175+48_1175+51del		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1175+48_1175+51del		intron_variant		1	NM_001352171.3	P1
	ENST00000671114.1	n.71-3781_71-3778del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0631 AC: 5979 AN: 94714 Hom.: 163 Cov.: 0

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0272

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0523

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0562

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0575

GnomAD4 exome AF: 0.0317 AC: 40740 AN: 1284824 Hom.: 169 AF XY: 0.0325 AC XY: 20468 AN XY: 630030

Gnomad4 AFR exome AF: 0.0545

Gnomad4 AMR exome AF: 0.0383

Gnomad4 ASJ exome AF: 0.0352

Gnomad4 EAS exome AF: 0.0818

Gnomad4 SAS exome AF: 0.0692

Gnomad4 FIN exome AF: 0.0219

Gnomad4 NFE exome AF: 0.0270

Gnomad4 OTH exome AF: 0.0380

GnomAD4 genome AF: 0.0633 AC: 5996 AN: 94778 Hom.: 165 Cov.: 0 AF XY: 0.0658 AC XY: 3021 AN XY: 45878

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0698

Gnomad4 ASJ AF: 0.0523

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0317

Gnomad4 NFE AF: 0.0399

Gnomad4 OTH AF: 0.0612

Alfa AF: 0.0323 Hom.: 3

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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs59771932; hg19: chr12-105260158;