2-27260233-G-T

Variant names:

• chr2-27260233-G-T
• rs11126936
• NM_003459.5:c.96-1299C>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.96-1299C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,974 control chromosomes in the GnomAD database, including 12,467 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 0.36 (12467 hom., cov: 31)
• Consequence: SLC30A3 NM_003459.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 20 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003459.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC30A3	NM_003459.5	MANE Select	c.96-1299C>A		intron	N/A	NP_003450.2
	SLC30A3	NM_001318949.2		c.81-1299C>A		intron	N/A	NP_001305878.1
	SLC30A3	NM_001318950.2		c.57-1299C>A		intron	N/A	NP_001305879.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC30A3	ENST00000233535.9	TSL:1 MANE Select	c.96-1299C>A		intron	N/A	ENSP00000233535.4
	SLC30A3	ENST00000961398.1		c.96-1299C>A		intron	N/A	ENSP00000631457.1
	SLC30A3	ENST00000940634.1		c.96-1900C>A		intron	N/A	ENSP00000610693.1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54788 AN: 151856 Hom.: 12417 Cov.: 31

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.361 AC: 54908 AN: 151974 Hom.: 12467 Cov.: 31 AF XY: 0.358 AC XY: 26617 AN XY: 74286

African (AFR) AF: 0.630 AC: 26117 AN: 41432

American (AMR) AF: 0.419 AC: 6390 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3468

East Asian (EAS) AF: 0.142 AC: 737 AN: 5174

South Asian (SAS) AF: 0.341 AC: 1637 AN: 4806

European-Finnish (FIN) AF: 0.202 AC: 2130 AN: 10566

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15780 AN: 67962

Other (OTH) AF: 0.347 AC: 730 AN: 2102

Alfa AF: 0.256 Hom.: 2314

Bravo AF: 0.391

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.85
PhyloP100		-0.83
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: rs11126936; hg19: chr2-27483101;