rs10778354

Positions:

• chr12-104894066-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001352171.3(SLC41A2):​c.735+1208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,898 control chromosomes in the GnomAD database, including 19,723 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 0.50 (19723 hom., cov: 31)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC41A2	NM_001352171.3	c.735+1208C>T		intron_variant		ENST00000258538.8	NP_001339100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC41A2	ENST00000258538.8	c.735+1208C>T		intron_variant		1	NM_001352171.3	ENSP00000258538	P1
SLC41A2	ENST00000437220.1	c.302+1208C>T		intron_variant		5		ENSP00000391377

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76601 AN: 151778 Hom.: 19707 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.505 AC: 76645 AN: 151898 Hom.: 19723 Cov.: 31 AF XY: 0.499 AC XY: 37059 AN XY: 74244

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.531

Alfa AF: 0.514 Hom.: 2706

Bravo AF: 0.514

Asia WGS AF: 0.315 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	13
DANN	Benign	0.94

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: rs10778354; hg19: chr12-105287844;