5-69100937-TG-TGGG

Variant names:

• chr5-69100937-T-TGG
• rs397840868
• NM_022902.5:c.206+16_206+17dupGG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_022902.5(SLC30A5):​c.206+16_206+17dupGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000442 in 1,414,704 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00074 (0 hom., cov: 26)
  • Exomes 𝑓: 0.00041 (0 hom.)
• Consequence: SLC30A5 NM_022902.5 intron
• Clinical Significance: Not reported in ClinVar
• 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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC30A5	NM_022902.5	c.206+16_206+17dupGG		intron_variant	Intron 2 of 15	ENST00000396591.8	NP_075053.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC30A5	ENST00000396591.8	c.206+8_206+9insGG		intron_variant	Intron 2 of 15	1	NM_022902.5	ENSP00000379836.3
SLC30A5	ENST00000380860.8	c.206+8_206+9insGG		intron_variant	Intron 2 of 3	1		ENSP00000370241.4
SLC30A5	ENST00000502979.1	c.84-2125_84-2124insGG		intron_variant	Intron 1 of 2	1		ENSP00000421251.1
SLC30A5	ENST00000504103.5	c.84-2125_84-2124insGG		intron_variant	Intron 1 of 2	3		ENSP00000426751.1

Frequencies

GnomAD3 genomes AF: 0.000745 AC: 111 AN: 149020 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.000147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000537

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00101

Gnomad SAS AF: 0.00517

Gnomad FIN AF: 0.000302

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.000879

Gnomad OTH AF: 0.00148

GnomAD3 exomes AF: 0.000479 AC: 86 AN: 179504 Hom.: 0 AF XY: 0.000518 AC XY: 51 AN XY: 98396

Gnomad AFR exome AF: 0.000153

Gnomad AMR exome AF: 0.000221

Gnomad ASJ exome AF: 0.000160

Gnomad EAS exome AF: 0.000633

Gnomad SAS exome AF: 0.00201

Gnomad FIN exome AF: 0.000110

Gnomad NFE exome AF: 0.000330

Gnomad OTH exome AF: 0.000255

GnomAD4 exome AF: 0.000408 AC: 516 AN: 1265570 Hom.: 0 Cov.: 29 AF XY: 0.000438 AC XY: 275 AN XY: 628278

Gnomad4 AFR exome AF: 0.000105

Gnomad4 AMR exome AF: 0.000206

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000270

Gnomad4 SAS exome AF: 0.00157

Gnomad4 FIN exome AF: 0.000106

Gnomad4 NFE exome AF: 0.000358

Gnomad4 OTH exome AF: 0.000411

GnomAD4 genome AF: 0.000738 AC: 110 AN: 149134 Hom.: 0 Cov.: 26 AF XY: 0.000812 AC XY: 59 AN XY: 72616

Gnomad4 AFR AF: 0.000147

Gnomad4 AMR AF: 0.000537

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00101

Gnomad4 SAS AF: 0.00517

Gnomad4 FIN AF: 0.000302

Gnomad4 NFE AF: 0.000879

Gnomad4 OTH AF: 0.00146

ClinVar

Not reported in ClinVar

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: rs397840868; hg19: chr5-68396764;