12-104866587-TAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant names:

• chr12-104866587-T-TAAAAAAAAAAAAAAAAAAAA
• rs34984157
• NM_001352171.3:c.1028-9_1028-8insTTTTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001352171.3(SLC41A2):​c.1028-9_1028-8insTTTTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 8.3e-7 (0 hom.)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352171.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC41A2	NM_001352171.3	MANE Select	c.1028-9_1028-8insTTTTTTTTTTTTTTTTTTTT		intron	N/A	NP_001339100.1	Q96JW4
	SLC41A2	NM_001352169.2		c.1028-9_1028-8insTTTTTTTTTTTTTTTTTTTT		intron	N/A	NP_001339098.1	Q96JW4
	SLC41A2	NM_001352170.3		c.1028-9_1028-8insTTTTTTTTTTTTTTTTTTTT		intron	N/A	NP_001339099.1	Q96JW4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC41A2	ENST00000258538.8	TSL:1 MANE Select	c.1028-9_1028-8insTTTTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000258538.3	Q96JW4
	SLC41A2	ENST00000906846.1		c.1028-9_1028-8insTTTTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000576905.1
	SLC41A2	ENST00000906847.1		c.1028-9_1028-8insTTTTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000576906.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 8.32e-7 AC: 1 AN: 1201800 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 597884

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 26800

American (AMR) AF: 0.00 AC: 0 AN: 27106

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20394

East Asian (EAS) AF: 0.00 AC: 0 AN: 36362

South Asian (SAS) AF: 0.00 AC: 0 AN: 61968

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36060

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4018

European-Non Finnish (NFE) AF: 0.00000106 AC: 1 AN: 939428

Other (OTH) AF: 0.00 AC: 0 AN: 49664

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs34984157; hg19: chr12-105260365;