rs950027

chr15-45508837-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013309.6(SLC30A4):c.538+2301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,092 control chromosomes in the GnomAD database, including 33,698 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (33698 hom., cov: 32)
• Consequence: SLC30A4 NM_013309.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

Genes affected

SLC30A4 (HGNC:11015): (solute carrier family 30 member 4) Zinc is the second most abundant trace metal in the human body. It is an essential element, serving both a structural role, as in the formation of zinc fingers in DNA-binding proteins, and a catalytic role in metalloenzymes, such as pancreatic carboxypeptidases (e.g., MIM 114852), alkaline phosphatases (e.g., MIM 171760), various dehydrogenases, and superoxide dismutases (e.g., MIM 147450). SLC30A4, or ZNT4, belongs to the ZNT family of zinc transporters. ZNTs are involved in transporting zinc out of the cytoplasm and have similar structures, consisting of 6 transmembrane domains and a histidine-rich cytoplasmic loop (Huang and Gitschier, 1997 [PubMed 9354792]).[supplied by OMIM, Mar 2008]

SLC30A4-AS1 (HGNC:56661): (SLC30A4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A4	NM_013309.6	c.538+2301A>G		intron_variant		ENST00000261867.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A4	ENST00000261867.5	c.538+2301A>G		intron_variant		1	NM_013309.6	P1
SLC30A4-AS1	ENST00000560647.5	n.556-3536T>C		intron_variant, non_coding_transcript_variant		3
SLC30A4	ENST00000559667.2	n.420+2301A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96908 AN: 151974 Hom.: 33623 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.614

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.638 AC: 97045 AN: 152092 Hom.: 33698 Cov.: 32 AF XY: 0.642 AC XY: 47748 AN XY: 74336

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.619

Alfa AF: 0.514 Hom.: 20517

Bravo AF: 0.665

Asia WGS AF: 0.777 AC: 2696 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.4
Dann	Benign	0.48

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: rs950027; hg19: chr15-45801035;