chr12-104846170-A-C

Position:

• chr12-104846170-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.1256-196T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 152,294 control chromosomes in the GnomAD database, including 89 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.024 (89 hom., cov: 32)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.10

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 12-104846170-A-C is Benign according to our data. Variant chr12-104846170-A-C is described in ClinVar as [Benign]. Clinvar id is 1243116.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1256-196T>G		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1256-196T>G		intron_variant		1	NM_001352171.3	P1

Frequencies

GnomAD3 genomes AF: 0.0239 AC: 3635 AN: 152176 Hom.: 89 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0186

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

GnomAD4 genome AF: 0.0239 AC: 3636 AN: 152294 Hom.: 89 Cov.: 32 AF XY: 0.0266 AC XY: 1980 AN XY: 74476

Gnomad4 AFR AF: 0.0269

Gnomad4 AMR AF: 0.0236

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.0947

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0117

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.0187 Hom.: 5

Bravo AF: 0.0216

Asia WGS AF: 0.0480 AC: 165 AN: 3476

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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.54

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: rs3816923; hg19: chr12-105239948;