chr12-104866737-A-C

Position:

• chr12-104866737-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001352171.3(SLC41A2):​c.1028-158T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0756 in 152,232 control chromosomes in the GnomAD database, including 493 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.076 (493 hom., cov: 32)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.51

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 12-104866737-A-C is Benign according to our data. Variant chr12-104866737-A-C is described in ClinVar as [Benign]. Clinvar id is 1239297.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1028-158T>G		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1028-158T>G		intron_variant		1	NM_001352171.3	P1
	ENST00000671114.1	n.71-3425A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0756 AC: 11506 AN: 152114 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0576

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0754

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.0789

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0756 AC: 11507 AN: 152232 Hom.: 493 Cov.: 32 AF XY: 0.0747 AC XY: 5561 AN XY: 74444

Gnomad4 AFR AF: 0.0538

Gnomad4 AMR AF: 0.0576

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.0756

Gnomad4 SAS AF: 0.0612

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.0941

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0815 Hom.: 61

Bravo AF: 0.0731

Asia WGS AF: 0.0630 AC: 220 AN: 3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.70

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

Other links and lift over

dbSNP: rs10861283; hg19: chr12-105260515;