rs7519615

Positions:

• chr1-219873960-C-T

Variant summary

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

The ENST00000484239.5(SLC30A10):​n.575+10166G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

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]

LOC105372926 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105372926	XR_001738474.1	n.173+10166G>A		intron_variant, non_coding_transcript_variant
LOC105372926	XR_001738475.1	n.173+10166G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A10	ENST00000484239.5	n.575+10166G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.00982

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.0270

Gnomad4 FIN AF: 0.00359

Gnomad4 NFE AF: 0.00615

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0362 Hom.: 243

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7519615; hg19: chr1-220047302;