Genetic Variant SLC41A2:c.1175+47_1175+50dupGTGT (chr12-104866381-T-TACAC) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001387131.1(SLC41A2):c.1222_1225dupGTGT(p.Tyr409CysfsTer12) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0053 ( 5 hom., cov: 0)

Exomes 𝑓: 0.0047 ( 2 hom. )

Consequence

SLC41A2
NM_001387131.1 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

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 Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3 link	c.1175+47_1175+50dupGTGT		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+50_1175+51insGTGT		intron_variant	Intron 7 of 10	1	NM_001352171.3	ENSP00000258538.3		Q96JW4
ENSG00000286410	ENST00000671114.1 link	n.71-3781_71-3780insACAC		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.00522

AC:

736

AN:

141004

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00792

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00391

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000847

Gnomad SAS

AF:

0.00473

Gnomad FIN

AF:

0.000931

Gnomad MID

AF:

0.00342

Gnomad NFE

AF:

0.00534

Gnomad OTH

AF:

0.00415

GnomAD4 exome

AF:

0.00465

AC:

5977

AN:

1284760

Hom.:

Cov.:

AF XY:

0.00459

AC XY:

2898

AN XY:

631396

show subpopulations

Gnomad4 AFR exome

AF:

0.00540

Gnomad4 AMR exome

AF:

0.00242

Gnomad4 ASJ exome

AF:

0.0000485

Gnomad4 EAS exome

AF:

0.000585

Gnomad4 SAS exome

AF:

0.00264

Gnomad4 FIN exome

AF:

0.000660

Gnomad4 NFE exome

AF:

0.00526

Gnomad4 OTH exome

AF:

0.00396

GnomAD4 genome

AF:

0.00527

AC:

744

AN:

141096

Hom.:

Cov.:

AF XY:

0.00516

AC XY:

354

AN XY:

68670

show subpopulations

Gnomad4 AFR

AF:

0.00812

Gnomad4 AMR

AF:

0.00391

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000849

Gnomad4 SAS

AF:

0.00474

Gnomad4 FIN

AF:

0.000931

Gnomad4 NFE

AF:

0.00534

Gnomad4 OTH

AF:

0.00411

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.

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