Variant 12-104866381-TACACACAC-T 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.1218_1225delGTGTGTGT(p.Cys407ArgfsTer10) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,112,090 control chromosomes in the GnomAD database, including 97 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.029 ( 107 hom., cov: 0)

Exomes 𝑓: 0.11 ( 97 hom. )

Failed GnomAD Quality Control

Consequence

SLC41A2
NM_001387131.1 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 12-104866381-TACACACAC-T is Benign according to our data. Variant chr12-104866381-TACACACAC-T is described in ClinVar as [Benign]. Clinvar id is 1259817.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3 link	c.1175+43_1175+50delGTGTGTGT		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+43_1175+50delGTGTGTGT		intron_variant	Intron 7 of 10	1	NM_001352171.3	ENSP00000258538.3		Q96JW4
ENSG00000286410	ENST00000671114.1 link	n.71-3780_71-3773delACACACAC		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0289

AC:

4064

AN:

140624

Hom.:

106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0503

Gnomad AMI

AF:

0.0116

Gnomad AMR

AF:

0.0260

Gnomad ASJ

AF:

0.0187

Gnomad EAS

AF:

0.157

Gnomad SAS

AF:

0.0156

Gnomad FIN

AF:

0.00952

Gnomad MID

AF:

0.0483

Gnomad NFE

AF:

0.0123

Gnomad OTH

AF:

0.0353

GnomAD3 exomes

AF:

0.155

AC:

23397

AN:

151248

Hom.:

AF XY:

0.156

AC XY:

12849

AN XY:

82436

show subpopulations

Gnomad AFR exome

AF:

0.131

Gnomad AMR exome

AF:

0.166

Gnomad ASJ exome

AF:

0.186

Gnomad EAS exome

AF:

0.201

Gnomad SAS exome

AF:

0.0959

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.163

Gnomad OTH exome

AF:

0.155

GnomAD4 exome

AF:

0.106

AC:

118319

AN:

1112090

Hom.:

AF XY:

0.108

AC XY:

59119

AN XY:

548570

show subpopulations

Gnomad4 AFR exome

AF:

0.0977

Gnomad4 AMR exome

AF:

0.161

Gnomad4 ASJ exome

AF:

0.158

Gnomad4 EAS exome

AF:

0.188

Gnomad4 SAS exome

AF:

0.0773

Gnomad4 FIN exome

AF:

0.103

Gnomad4 NFE exome

AF:

0.102

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0289

AC:

4069

AN:

140712

Hom.:

107

Cov.:

AF XY:

0.0296

AC XY:

2024

AN XY:

68444

show subpopulations

Gnomad4 AFR

AF:

0.0503

Gnomad4 AMR

AF:

0.0259

Gnomad4 ASJ

AF:

0.0187

Gnomad4 EAS

AF:

0.156

Gnomad4 SAS

AF:

0.0159

Gnomad4 FIN

AF:

0.00952

Gnomad4 NFE

AF:

0.0123

Gnomad4 OTH

AF:

0.0371

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over