12-104886079-AT-A

Variant summary

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

The NM_001352171.3(SLC41A2):c.1027+213del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 152,156 control chromosomes in the GnomAD database, including 476 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.074 (476 hom., cov: 31)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0920

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-104886079-AT-A is Benign according to our data. Variant chr12-104886079-AT-A is described in ClinVar as [Benign]. Clinvar id is 1251877.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1027+213del		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1027+213del		intron_variant		1	NM_001352171.3	P1

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11310 AN: 152038 Hom.: 477 Cov.: 31

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0749

Gnomad SAS AF: 0.0610

Gnomad FIN AF: 0.0747

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0785

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0743 AC: 11311 AN: 152156 Hom.: 476 Cov.: 31 AF XY: 0.0734 AC XY: 5459 AN XY: 74378

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.0750

Gnomad4 SAS AF: 0.0610

Gnomad4 FIN AF: 0.0747

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.0773

Alfa AF: 0.0360 Hom.: 30

Bravo AF: 0.0721

Asia WGS AF: 0.0600 AC: 210 AN: 3476

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

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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: rs67670868; hg19: chr12-105279857;