Genetic Variant SLC41A2:c.1175+39_1175+50delGTGTGTGTGTGT (chr12-104866381-TACACACACACAC-T) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3

The NM_001387131.1(SLC41A2):c.1214_1225delGTGTGTGTGTGT(p.Cys405_Val408del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000283 in 1,427,030 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00079 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00023 ( 0 hom. )

Consequence

SLC41A2
NM_001387131.1 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.94

Variant links:

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]

SLC41A2 links:

ENSG00000286410 (HGNC:):

ENSG00000286410 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP3

Nonframeshift variant in repetitive region in NM_001387131.1

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3 link	c.1175+39_1175+50delGTGTGTGTGTGT		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 link	c.1175+39_1175+50delGTGTGTGTGTGT		intron_variant	Intron 7 of 10	1	NM_001352171.3	ENSP00000258538.3		Q96JW4
ENSG00000286410	ENST00000671114.1 link	n.71-3780_71-3769delACACACACACAC		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.000787

AC:

111

AN:

141012

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00237

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000699

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00339

Gnomad SAS

AF:

0.000237

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000770

Gnomad OTH

AF:

0.000518

GnomAD4 exome

AF:

0.000228

AC:

293

AN:

1285926

Hom.:

AF XY:

0.000223

AC XY:

141

AN XY:

631918

show subpopulations

Gnomad4 AFR exome

AF:

0.00294

Gnomad4 AMR exome

AF:

0.000252

Gnomad4 ASJ exome

AF:

0.0000971

Gnomad4 EAS exome

AF:

0.00117

Gnomad4 SAS exome

AF:

0.000337

Gnomad4 FIN exome

AF:

0.0000733

Gnomad4 NFE exome

AF:

0.000115

Gnomad4 OTH exome

AF:

0.000342

GnomAD4 genome

AF:

0.000787

AC:

111

AN:

141104

Hom.:

Cov.:

AF XY:

0.000786

AC XY:

AN XY:

68670

show subpopulations

Gnomad4 AFR

AF:

0.00236

Gnomad4 AMR

AF:

0.0000698

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00340

Gnomad4 SAS

AF:

0.000237

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000770

Gnomad4 OTH

AF:

0.000514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

12-104866381-TACACACACACACACACACACAC-TACACACACAC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over