Variant 12-104866415-CAT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001387131.1(SLC41A2):c.1190_1191delAT(p.Tyr397CysfsTer22) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00573 in 1,530,446 control chromosomes in the GnomAD database, including 250 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.035 ( 231 hom., cov: 28)

Exomes 𝑓: 0.0029 ( 19 hom. )

Consequence

SLC41A2
NM_001387131.1 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.02

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 12-104866415-CAT-C is Benign according to our data. Variant chr12-104866415-CAT-C is described in ClinVar as [Benign]. Clinvar id is 1228445.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3 link	c.1175+15_1175+16delAT		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+15_1175+16delAT		intron_variant	Intron 7 of 10	1	NM_001352171.3	ENSP00000258538.3		Q96JW4
ENSG00000286410	ENST00000671114.1 link	n.71-3746_71-3745delAT		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0348

AC:

4766

AN:

136944

Hom.:

232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0156

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000223

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0105

Gnomad NFE

AF:

0.000612

Gnomad OTH

AF:

0.0231

GnomAD3 exomes

AF:

0.00793

AC:

1594

AN:

200884

Hom.:

AF XY:

0.00589

AC XY:

643

AN XY:

109172

show subpopulations

Gnomad AFR exome

AF:

0.0835

Gnomad AMR exome

AF:

0.00633

Gnomad ASJ exome

AF:

0.00417

Gnomad EAS exome

AF:

0.0000633

Gnomad SAS exome

AF:

0.00149

Gnomad FIN exome

AF:

0.00261

Gnomad NFE exome

AF:

0.00203

Gnomad OTH exome

AF:

0.00577

GnomAD4 exome

AF:

0.00286

AC:

3991

AN:

1393396

Hom.:

AF XY:

0.00253

AC XY:

1748

AN XY:

692274

show subpopulations

Gnomad4 AFR exome

AF:

0.0934

Gnomad4 AMR exome

AF:

0.00726

Gnomad4 ASJ exome

AF:

0.00194

Gnomad4 EAS exome

AF:

0.0000526

Gnomad4 SAS exome

AF:

0.00127

Gnomad4 FIN exome

AF:

0.00146

Gnomad4 NFE exome

AF:

0.000570

Gnomad4 OTH exome

AF:

0.00627

GnomAD4 genome

AF:

0.0349

AC:

4780

AN:

137050

Hom.:

231

Cov.:

AF XY:

0.0332

AC XY:

2216

AN XY:

66704

show subpopulations

Gnomad4 AFR

AF:

0.128

Gnomad4 AMR

AF:

0.0156

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000223

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000612

Gnomad4 OTH

AF:

0.0228

Alfa

AF:

0.000503

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 20, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over