Variant 4-102253164-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001135147.1(SLC39A8):c.*258G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 352,306 control chromosomes in the GnomAD database, including 55,575 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 22888 hom., cov: 26)

Exomes 𝑓: 0.56 ( 32687 hom. )

Consequence

SLC39A8
NM_001135147.1 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.97

Variant links:

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]

SLC39A8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 4-102253164-C-T is Benign according to our data. Variant chr4-102253164-C-T is described in ClinVar as [Benign]. Clinvar id is 1247122.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC39A8	NM_001135147.1 linkuse as main transcript	c.*258G>A		3_prime_UTR_variant	11/11		NP_001128619.1	Q9C0K1-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC39A8	ENST00000424970.7 linkuse as main transcript	n.*565G>A		non_coding_transcript_exon_variant	12/12	2		ENSP00000394548.3		A0A804HKX2
SLC39A8	ENST00000424970.7 linkuse as main transcript	n.*565G>A		3_prime_UTR_variant	12/12	2		ENSP00000394548.3		A0A804HKX2

Frequencies

GnomAD3 genomes

AF:

0.556

AC:

82447

AN:

148220

Hom.:

22865

Cov.:

show subpopulations

Gnomad AFR

AF:

0.563

Gnomad AMI

AF:

0.667

Gnomad AMR

AF:

0.514

Gnomad ASJ

AF:

0.664

Gnomad EAS

AF:

0.452

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.635

Gnomad NFE

AF:

0.578

Gnomad OTH

AF:

0.556

GnomAD4 exome

AF:

0.564

AC:

115042

AN:

203970

Hom.:

32687

Cov.:

AF XY:

0.567

AC XY:

58795

AN XY:

103746

show subpopulations

Gnomad4 AFR exome

AF:

0.565

Gnomad4 AMR exome

AF:

0.511

Gnomad4 ASJ exome

AF:

0.671

Gnomad4 EAS exome

AF:

0.409

Gnomad4 SAS exome

AF:

0.440

Gnomad4 FIN exome

AF:

0.515

Gnomad4 NFE exome

AF:

0.590

Gnomad4 OTH exome

AF:

0.574

GnomAD4 genome

AF:

0.556

AC:

82506

AN:

148336

Hom.:

22888

Cov.:

AF XY:

0.550

AC XY:

39759

AN XY:

72288

show subpopulations

Gnomad4 AFR

AF:

0.564

Gnomad4 AMR

AF:

0.513

Gnomad4 ASJ

AF:

0.664

Gnomad4 EAS

AF:

0.451

Gnomad4 SAS

AF:

0.427

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.578

Gnomad4 OTH

AF:

0.557

Alfa

AF:

0.425

Hom.:

1101

Bravo

AF:

0.555

Asia WGS

AF:

0.402

AC:

1399

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 27, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.73

DANN

Benign

0.56

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over