rs7519615

Variant names:

• chr1-219873960-C-T
• rs7519615
• ENST00000484239.5:n.575+10166G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484239.5(SLC30A10):​n.575+10166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.087 in 151,986 control chromosomes in the GnomAD database, including 1,443 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 0.087 (1443 hom., cov: 31)
• Consequence: SLC30A10 ENST00000484239.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 1 publications found

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]

SLC30A10 Gene-Disease associations (from GenCC):

• cirrhosis - dystonia - polycythemia - hypermanganesemia syndrome

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Genomics England PanelApp

LOC105372926 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372926	XR_001738474.1	n.173+10166G>A		intron_variant	Intron 1 of 5
LOC105372926	XR_001738475.1	n.173+10166G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC30A10	ENST00000484239.5	n.575+10166G>A		intron_variant	Intron 4 of 8	2

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13212 AN: 151868 Hom.: 1439 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.00982

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.00359

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.00615

Gnomad OTH AF: 0.0736

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

GnomAD4 genome AF: 0.0870 AC: 13230 AN: 151986 Hom.: 1443 Cov.: 31 AF XY: 0.0873 AC XY: 6486 AN XY: 74282

African (AFR) AF: 0.234 AC: 9696 AN: 41418

American (AMR) AF: 0.116 AC: 1774 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.00982 AC: 34 AN: 3464

East Asian (EAS) AF: 0.190 AC: 978 AN: 5150

South Asian (SAS) AF: 0.0270 AC: 130 AN: 4810

European-Finnish (FIN) AF: 0.00359 AC: 38 AN: 10594

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.00615 AC: 418 AN: 67980

Other (OTH) AF: 0.0728 AC: 154 AN: 2114

Alfa AF: 0.0358 Hom.: 334

Bravo AF: 0.107

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.63
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs7519615; hg19: chr1-220047302;