rs73924411

Variant names:

• chr2-27256635-C-T
• rs73924411
• NM_003459.5:c.884-115G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003459.5(SLC30A3):​c.884-115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0482 in 1,435,532 control chromosomes in the GnomAD database, including 1,850 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 0.056 (267 hom., cov: 32)
  • Exomes 𝑓: 0.047 (1583 hom.)
• Consequence: SLC30A3 NM_003459.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 9 publications found

Genes affected

SLC30A3 (HGNC:11014): (solute carrier family 30 member 3) Predicted to enable zinc ion transmembrane transporter activity. Involved in regulation of sequestering of zinc ion. Located in late endosome and synaptic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC30A3	NM_003459.5	c.884-115G>A		intron_variant	Intron 6 of 7	ENST00000233535.9	NP_003450.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC30A3	ENST00000233535.9	c.884-115G>A		intron_variant	Intron 6 of 7	1	NM_003459.5	ENSP00000233535.4

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8453 AN: 152076 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0417

Gnomad ASJ AF: 0.0312

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0502

Gnomad OTH AF: 0.0578

GnomAD4 exome AF: 0.0473 AC: 60721 AN: 1283338 Hom.: 1583 Cov.: 18 AF XY: 0.0478 AC XY: 30561 AN XY: 639032

African (AFR) AF: 0.0803 AC: 2406 AN: 29968

American (AMR) AF: 0.0336 AC: 1352 AN: 40206

Ashkenazi Jewish (ASJ) AF: 0.0275 AC: 629 AN: 22912

East Asian (EAS) AF: 0.0000788 AC: 3 AN: 38060

South Asian (SAS) AF: 0.0624 AC: 4835 AN: 77512

European-Finnish (FIN) AF: 0.0368 AC: 1881 AN: 51078

Middle Eastern (MID) AF: 0.0677 AC: 334 AN: 4934

European-Non Finnish (NFE) AF: 0.0484 AC: 46653 AN: 964776

Other (OTH) AF: 0.0488 AC: 2628 AN: 53892

GnomAD4 genome AF: 0.0555 AC: 8449 AN: 152194 Hom.: 267 Cov.: 32 AF XY: 0.0540 AC XY: 4016 AN XY: 74416

African (AFR) AF: 0.0821 AC: 3405 AN: 41482

American (AMR) AF: 0.0417 AC: 637 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0312 AC: 108 AN: 3466

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5178

South Asian (SAS) AF: 0.0565 AC: 273 AN: 4830

European-Finnish (FIN) AF: 0.0339 AC: 360 AN: 10616

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0502 AC: 3415 AN: 68012

Other (OTH) AF: 0.0572 AC: 121 AN: 2116

Alfa AF: 0.0563 Hom.: 36

Bravo AF: 0.0575

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.78
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs73924411; hg19: chr2-27479503;