5-69100937-T-TG

Variant summary

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

The NM_022902.5(SLC30A5):c.206+17dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 148,588 control chromosomes in the GnomAD database, including 2,443 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (2443 hom., cov: 26)
  • Exomes 𝑓: 0.14 (1424 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC30A5 NM_022902.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.402

Genes affected

SLC30A5 (HGNC:19089): (solute carrier family 30 member 5) This gene encodes a member of the SLC30A/ZnT family of zinc transporter proteins. ZnT proteins mediate both cellular zinc efflux and zinc sequestration into membrane-bound organelles. The encoded protein plays a role in the early secretory pathway as a heterodimer with zinc transporter 6, and may also regulate zinc sequestration into secretory granules of pancreatic beta cells. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 19. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-69100937-T-TG is Benign according to our data. Variant chr5-69100937-T-TG is described in ClinVar as [Benign]. Clinvar id is 769300.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A5	NM_022902.5	c.206+17dup		intron_variant		ENST00000396591.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A5	ENST00000396591.8	c.206+17dup		intron_variant		1	NM_022902.5	P1
SLC30A5	ENST00000380860.8	c.206+17dup		intron_variant		1
SLC30A5	ENST00000502979.1	c.84-2116dup		intron_variant		1
SLC30A5	ENST00000504103.5	c.84-2116dup		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25102 AN: 148476 Hom.: 2443 Cov.: 26

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.186

GnomAD3 exomes AF: 0.175 AC: 31354 AN: 179504 Hom.: 249 AF XY: 0.176 AC XY: 17327 AN XY: 98396

Gnomad AFR exome AF: 0.0520

Gnomad AMR exome AF: 0.158

Gnomad ASJ exome AF: 0.178

Gnomad EAS exome AF: 0.289

Gnomad SAS exome AF: 0.152

Gnomad FIN exome AF: 0.160

Gnomad NFE exome AF: 0.188

Gnomad OTH exome AF: 0.176

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.144 AC: 174879 AN: 1218220 Hom.: 1424 Cov.: 29 AF XY: 0.143 AC XY: 86459 AN XY: 604960

Gnomad4 AFR exome AF: 0.0382

Gnomad4 AMR exome AF: 0.132

Gnomad4 ASJ exome AF: 0.132

Gnomad4 EAS exome AF: 0.206

Gnomad4 SAS exome AF: 0.108

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.148

Gnomad4 OTH exome AF: 0.142

GnomAD4 genome AF: 0.169 AC: 25097 AN: 148588 Hom.: 2443 Cov.: 26 AF XY: 0.166 AC XY: 12009 AN XY: 72322

Gnomad4 AFR AF: 0.0644

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.184

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

Invitae

Aug 16, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs397840868; hg19: chr5-68396764;