1-219914320-TG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018713.3(SLC30A10):c.*1128del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,282 control chromosomes in the GnomAD database, including 1,111 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (1111 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC30A10 NM_018713.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0910

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 -10 ACMG points.

• BP6: Variant 1-219914320-TG-T is Benign according to our data. Variant chr1-219914320-TG-T is described in ClinVar as [Benign]. Clinvar id is 295575.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A10	NM_018713.3	c.*1128del		3_prime_UTR_variant	4/4	ENST00000366926.4
SLC30A10	NM_001376929.1	c.*1128del		3_prime_UTR_variant	4/4
SLC30A10	NM_001416004.1	c.*1128del		3_prime_UTR_variant	3/3
SLC30A10	NM_001416005.1	c.*1128del		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A10	ENST00000366926.4	c.*1128del		3_prime_UTR_variant	4/4	1	NM_018713.3	P3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16165 AN: 152164 Hom.: 1110 Cov.: 31

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.114

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.106 AC: 16169 AN: 152282 Hom.: 1111 Cov.: 31 AF XY: 0.109 AC XY: 8103 AN XY: 74448

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0970

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.112

Alfa AF: 0.118 Hom.: 143

Bravo AF: 0.104

Asia WGS AF: 0.182 AC: 631 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hypermanganesemia with dystonia, polycythemia, and cirrhosis Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59755757; hg19: chr1-220087662;