rs950027

Variant names:

• chr15-45508837-T-C
• rs950027
• NM_013309.6:c.538+2301A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC30A4	NM_013309.6	c.538+2301A>G		intron_variant	Intron 3 of 7	ENST00000261867.5	NP_037441.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC30A4	ENST00000261867.5	c.538+2301A>G		intron_variant	Intron 3 of 7	1	NM_013309.6	ENSP00000261867.3

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

African (AFR) AF: 0.898 AC: 37275 AN: 41530

American (AMR) AF: 0.677 AC: 10340 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1905 AN: 3466

East Asian (EAS) AF: 0.929 AC: 4806 AN: 5174

South Asian (SAS) AF: 0.701 AC: 3376 AN: 4818

European-Finnish (FIN) AF: 0.477 AC: 5036 AN: 10550

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32529 AN: 67974

Other (OTH) AF: 0.619 AC: 1303 AN: 2106

Alfa AF: 0.537 Hom.: 57836

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
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs950027; hg19: chr15-45801035;