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12-104805260-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_001352171.3(SLC41A2):c.1614C>T(p.Ser538=) 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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=2.16 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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/exons MANE UniProt
SLC41A2NM_001352171.3 linkuse as main transcriptc.1614C>T p.Ser538= synonymous_variant 11/11 ENST00000258538.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC41A2ENST00000258538.8 linkuse as main transcriptc.1614C>T p.Ser538= synonymous_variant 11/111 NM_001352171.3 P1
SLC41A2ENST00000549713.1 linkuse as main transcriptn.167C>T non_coding_transcript_exon_variant 2/23

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0877
AC:
13344
AN:
152092
Hom.:
639
Cov.:
32
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.:
31
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0878
AC:
13365
AN:
152210
Hom.:
641
Cov.:
32
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:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 04, 2021- -

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.

Other links and lift over

dbSNP: rs11112201; hg19: chr12-105199038; COSMIC: COSV51603260; API