dbSNP rs73924411: SLC30A3:c.884-115G>A (chr2-27256635-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.203

Publications

9 publications found

Variant links:

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]

SLC30A3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC30A3	NM_003459.5	MANE Select	c.884-115G>A	intron	N/A	NP_003450.2
SLC30A3	NM_001318949.2		c.869-115G>A	intron	N/A	NP_001305878.1
SLC30A3	NM_001318950.2		c.845-115G>A	intron	N/A	NP_001305879.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC30A3	ENST00000233535.9	TSL:1 MANE Select	c.884-115G>A	intron	N/A	ENSP00000233535.4	Q99726
SLC30A3	ENST00000961398.1		c.773-115G>A	intron	N/A	ENSP00000631457.1
SLC30A3	ENST00000940634.1		c.728-115G>A	intron	N/A	ENSP00000610693.1

Frequencies

GnomAD3 genomes

AF:

0.0556

AC:

8453

AN:

152076

Hom.:

267

Cov.:

show subpopulations

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.:

AF XY:

0.0478

AC XY:

30561

AN XY:

639032

show subpopulations

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:

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

2923

5846

8769

11692

14615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1690

3380

5070

6760

8450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0555

AC:

8449

AN:

152194

Hom.:

267

Cov.:

AF XY:

0.0540

AC XY:

4016

AN XY:

74416

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0502

AC:

3415

AN:

68012

Other (OTH)

AF:

0.0572

AC:

121

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

401

801

1202

1602

2003

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0563

Hom.:

Bravo

AF:

0.0575

Asia WGS

AF:

0.0240

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.3

(source)

DANN

Benign

0.78

PhyloP100

0.20

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over