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rs12582312

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001352171.3(SLC41A2):​c.1537-16065G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0245 in 152,068 control chromosomes in the GnomAD database, including 96 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.025 ( 96 hom., cov: 32)

Consequence

SLC41A2
NM_001352171.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.277
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC41A2NM_001352171.3 linkuse as main transcriptc.1537-16065G>A intron_variant ENST00000258538.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC41A2ENST00000258538.8 linkuse as main transcriptc.1537-16065G>A intron_variant 1 NM_001352171.3 P1
SLC41A2ENST00000549713.1 linkuse as main transcriptn.89+12689G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0245
AC:
3726
AN:
151950
Hom.:
96
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0399
Gnomad AMI
AF:
0.0110
Gnomad AMR
AF:
0.0213
Gnomad ASJ
AF:
0.0127
Gnomad EAS
AF:
0.154
Gnomad SAS
AF:
0.0147
Gnomad FIN
AF:
0.00503
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0103
Gnomad OTH
AF:
0.0274
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0245
AC:
3727
AN:
152068
Hom.:
96
Cov.:
32
AF XY:
0.0247
AC XY:
1834
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.0398
Gnomad4 AMR
AF:
0.0213
Gnomad4 ASJ
AF:
0.0127
Gnomad4 EAS
AF:
0.153
Gnomad4 SAS
AF:
0.0149
Gnomad4 FIN
AF:
0.00503
Gnomad4 NFE
AF:
0.0103
Gnomad4 OTH
AF:
0.0295
Alfa
AF:
0.0174
Hom.:
4
Bravo
AF:
0.0292
Asia WGS
AF:
0.0630
AC:
220
AN:
3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.1
DANN
Benign
0.75

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: rs12582312; hg19: chr12-105215180; API