Variant 12-104805260-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001352171.3(SLC41A2):c.1614C>T(p.Ser538Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0906 in 1,613,468 control chromosomes in the GnomAD database, including 6,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.088 ( 641 hom., cov: 32)

Exomes 𝑓: 0.091 ( 6118 hom. )

Consequence

SLC41A2
NM_001352171.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.16

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 12-104805260-G-A is Benign according to our data. Variant chr12-104805260-G-A is described in ClinVar as [Benign]. Clinvar id is 1183921.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.16 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3 link	c.1614C>T	p.Ser538Ser	synonymous_variant	Exon 11 of 11	ENST00000258538.8	NP_001339100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC41A2	ENST00000258538.8 link	c.1614C>T	p.Ser538Ser	synonymous_variant	Exon 11 of 11	1	NM_001352171.3	ENSP00000258538.3		Q96JW4
SLC41A2	ENST00000549713.1 link	n.167C>T		non_coding_transcript_exon_variant	Exon 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.0877

AC:

13344

AN:

152092

Hom.:

639

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0852

Gnomad AMI

AF:

0.0844

Gnomad AMR

AF:

0.0645

Gnomad ASJ

AF:

0.0579

Gnomad EAS

AF:

0.0821

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.0775

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0965

Gnomad OTH

AF:

0.0918

GnomAD3 exomes

AF:

0.0850

AC:

21337

AN:

250970

Hom.:

993

AF XY:

0.0889

AC XY:

12058

AN XY:

135640

show subpopulations

Gnomad AFR exome

AF:

0.0814

Gnomad AMR exome

AF:

0.0478

Gnomad ASJ exome

AF:

0.0604

Gnomad EAS exome

AF:

0.0797

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.0779

Gnomad NFE exome

AF:

0.0937

Gnomad OTH exome

AF:

0.0870

GnomAD4 exome

AF:

0.0909

AC:

132756

AN:

1461258

Hom.:

6118

Cov.:

AF XY:

0.0917

AC XY:

66646

AN XY:

726952

show subpopulations

Gnomad4 AFR exome

AF:

0.0840

Gnomad4 AMR exome

AF:

0.0515

Gnomad4 ASJ exome

AF:

0.0565

Gnomad4 EAS exome

AF:

0.0940

Gnomad4 SAS exome

AF:

0.108

Gnomad4 FIN exome

AF:

0.0786

Gnomad4 NFE exome

AF:

0.0924

Gnomad4 OTH exome

AF:

0.0936

GnomAD4 genome

AF:

0.0878

AC:

13365

AN:

152210

Hom.:

641

Cov.:

AF XY:

0.0871

AC XY:

6481

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0855

Gnomad4 AMR

AF:

0.0645

Gnomad4 ASJ

AF:

0.0579

Gnomad4 EAS

AF:

0.0823

Gnomad4 SAS

AF:

0.105

Gnomad4 FIN

AF:

0.0775

Gnomad4 NFE

AF:

0.0966

Gnomad4 OTH

AF:

0.0932

Alfa

AF:

0.0898

Hom.:

681

Bravo

AF:

0.0850

Asia WGS

AF:

0.109

AC:

378

AN:

3476

EpiCase

AF:

0.0956

EpiControl

AF:

0.0964

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 04, 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

BayesDel_noAF

Benign

-0.46

CADD

Benign

8.6

DANN

Benign

0.69

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