rs12064812

chr1-219925018-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018713.3(SLC30A10):c.718+2010A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,026 control chromosomes in the GnomAD database, including 6,685 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 0.28 (6685 hom., cov: 31)
• Consequence: SLC30A10 NM_018713.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

SLC30A10 (HGNC:25355): (solute carrier family 30 member 10) This gene is highly expressed in the liver and is inducible by manganese. Its protein product appears to be critical in maintaining manganese levels, and has higher specificity for manganese than zinc. Loss of function mutations appear to result in a pleomorphic phenotype, including dystonia and adult-onset parkinsonism. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Mar 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A10	NM_018713.3	c.718+2010A>G		intron_variant		ENST00000366926.4
SLC30A10	NM_001376929.1	c.529+2010A>G		intron_variant
SLC30A10	NM_001416004.1	c.43+2010A>G		intron_variant
SLC30A10	NM_001416005.1	c.43+2010A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A10	ENST00000366926.4	c.718+2010A>G		intron_variant		1	NM_018713.3	P3
SLC30A10	ENST00000356609.2	c.*84+2010A>G		intron_variant, NMD_transcript_variant		1
SLC30A10	ENST00000696608.1	c.529+2010A>G		intron_variant				A2
SLC30A10	ENST00000484239.5	n.158+2010A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43030 AN: 151908 Hom.: 6681 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.283 AC: 43034 AN: 152026 Hom.: 6685 Cov.: 31 AF XY: 0.289 AC XY: 21450 AN XY: 74294

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.284

Alfa AF: 0.312 Hom.: 989

Bravo AF: 0.269

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.99
Dann	Benign	0.40

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: rs12064812; hg19: chr1-220098360; COSMIC: COSV63070742;