12-104866587-TAAAAAAAAA-TAAAAA

Variant names:

• chr12-104866587-TAAAA-T
• rs34984157
• NM_001352171.3:c.1028-12_1028-9delTTTT

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_001352171.3(SLC41A2):​c.1028-12_1028-9delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00257 in 1,333,796 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000036 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0029 (0 hom.)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

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]

ENSG00000286410 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.00286 (3425/1195580) while in subpopulation EAS AF= 0.0208 (748/35890). AF 95% confidence interval is 0.0196. There are 0 homozygotes in gnomad4_exome. There are 1776 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3	c.1028-12_1028-9delTTTT		intron_variant	Intron 6 of 10	ENST00000258538.8	NP_001339100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1028-12_1028-9delTTTT		intron_variant	Intron 6 of 10	1	NM_001352171.3	ENSP00000258538.3
ENSG00000286410	ENST00000671114.1	n.71-3574_71-3571delAAAA		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0000362 AC: 5 AN: 138216 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000263

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000206

Gnomad SAS AF: 0.000232

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000315

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00782 AC: 979 AN: 125200 Hom.: 0 AF XY: 0.00752 AC XY: 522 AN XY: 69374

Gnomad AFR exome AF: 0.00708

Gnomad AMR exome AF: 0.0140

Gnomad ASJ exome AF: 0.00682

Gnomad EAS exome AF: 0.0247

Gnomad SAS exome AF: 0.00859

Gnomad FIN exome AF: 0.00474

Gnomad NFE exome AF: 0.00389

Gnomad OTH exome AF: 0.00723

GnomAD4 exome AF: 0.00286 AC: 3425 AN: 1195580 Hom.: 0 AF XY: 0.00299 AC XY: 1776 AN XY: 594698

Gnomad4 AFR exome AF: 0.00594

Gnomad4 AMR exome AF: 0.0102

Gnomad4 ASJ exome AF: 0.00369

Gnomad4 EAS exome AF: 0.0208

Gnomad4 SAS exome AF: 0.00540

Gnomad4 FIN exome AF: 0.00351

Gnomad4 NFE exome AF: 0.00166

Gnomad4 OTH exome AF: 0.00308

GnomAD4 genome AF: 0.0000362 AC: 5 AN: 138216 Hom.: 0 Cov.: 0 AF XY: 0.0000300 AC XY: 2 AN XY: 66600

Gnomad4 AFR AF: 0.0000263

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000206

Gnomad4 SAS AF: 0.000232

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000315

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs34984157; hg19: chr12-105260365;