rs1153831

chr15-45480250-G-A

Variant summary

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

The NM_013309.6(SLC30A4):c.*4913C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,100 control chromosomes in the GnomAD database, including 4,724 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 0.21 (4724 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC30A4 NM_013309.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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 (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A4	NM_013309.6	c.*4913C>T		3_prime_UTR_variant	8/8	ENST00000261867.5
SLC30A4	XM_017022560.3	c.*4913C>T		3_prime_UTR_variant	7/7
SLC30A4-AS1	XR_007064610.1	n.4395G>A		non_coding_transcript_exon_variant	4/4
SLC30A4-AS1	XR_007064611.1	n.1913+3698G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A4	ENST00000261867.5	c.*4913C>T		3_prime_UTR_variant	8/8	1	NM_013309.6	P1
SLC30A4-AS1	ENST00000560647.5	n.555+3698G>A		intron_variant, non_coding_transcript_variant		3
SLC30A4-AS1	ENST00000558536.5	n.546+3698G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31304 AN: 151982 Hom.: 4705 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0803

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.194

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.206 AC: 31365 AN: 152100 Hom.: 4724 Cov.: 32 AF XY: 0.203 AC XY: 15108 AN XY: 74376

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0803

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.192

Alfa AF: 0.131 Hom.: 2297

Bravo AF: 0.221

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.017
Dann	Benign	0.25

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: rs1153831; hg19: chr15-45772448;