4-102253159-C-CG

Variant summary

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

The NM_001135147.1(SLC39A8):c.*262_*263insC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.81 (50076 hom., cov: 0)
  • Exomes 𝑓: 0.76 (57681 hom.)
• Consequence: SLC39A8 NM_001135147.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.96

Genes affected

SLC39A8 (HGNC:20862): (solute carrier family 39 member 8) This gene encodes a member of the SLC39 family of solute-carrier genes, which show structural characteristics of zinc transporters. The encoded protein is glycosylated and found in the plasma membrane and mitochondria, and functions in the cellular import of zinc at the onset of inflammation. It is also thought to be the primary transporter of the toxic cation cadmium, which is found in cigarette smoke. Multiple transcript variants encoding different isoforms have been found for this gene. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-102253159-C-CG is Benign according to our data. Variant chr4-102253159-C-CG is described in ClinVar as [Benign]. Clinvar id is 1247560.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A8	NM_001135147.1	c.*262_*263insC		3_prime_UTR_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A8	ENST00000424970.7	c.*569_*570insC		3_prime_UTR_variant, NMD_transcript_variant	12/12	2

Frequencies

GnomAD3 genomes AF: 0.809 AC: 121463 AN: 150048 Hom.: 50027 Cov.: 0

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.784

GnomAD4 exome AF: 0.762 AC: 148517 AN: 194824 Hom.: 57681 Cov.: 0 AF XY: 0.765 AC XY: 75748 AN XY: 98962

Gnomad4 AFR exome AF: 0.956

Gnomad4 AMR exome AF: 0.666

Gnomad4 ASJ exome AF: 0.843

Gnomad4 EAS exome AF: 0.507

Gnomad4 SAS exome AF: 0.775

Gnomad4 FIN exome AF: 0.734

Gnomad4 NFE exome AF: 0.790

Gnomad4 OTH exome AF: 0.774

GnomAD4 genome AF: 0.809 AC: 121555 AN: 150166 Hom.: 50076 Cov.: 0 AF XY: 0.802 AC XY: 58688 AN XY: 73154

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.785

Alfa AF: 0.807 Hom.: 5363

Asia WGS AF: 0.624 AC: 2171 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

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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: rs11382393; hg19: chr4-103174316;