rs73924411

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000233535.9(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
ENST00000233535.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.203
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
SLC30A3NM_003459.5 linkuse as main transcriptc.884-115G>A intron_variant ENST00000233535.9 NP_003450.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC30A3ENST00000233535.9 linkuse as main transcriptc.884-115G>A intron_variant 1 NM_003459.5 ENSP00000233535 P1
SLC30A3ENST00000445870.5 linkuse as main transcriptc.695-115G>A intron_variant 5 ENSP00000388219
SLC30A3ENST00000482990.1 linkuse as main transcriptn.774-115G>A intron_variant, non_coding_transcript_variant 2
SLC30A3ENST00000497341.5 linkuse as main transcriptn.1537-115G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0556
AC:
8453
AN:
152076
Hom.:
267
Cov.:
32
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.:
18
AF XY:
0.0478
AC XY:
30561
AN XY:
639032
show subpopulations
Gnomad4 AFR exome
AF:
0.0803
Gnomad4 AMR exome
AF:
0.0336
Gnomad4 ASJ exome
AF:
0.0275
Gnomad4 EAS exome
AF:
0.0000788
Gnomad4 SAS exome
AF:
0.0624
Gnomad4 FIN exome
AF:
0.0368
Gnomad4 NFE exome
AF:
0.0484
Gnomad4 OTH exome
AF:
0.0488
GnomAD4 genome
AF:
0.0555
AC:
8449
AN:
152194
Hom.:
267
Cov.:
32
AF XY:
0.0540
AC XY:
4016
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0821
Gnomad4 AMR
AF:
0.0417
Gnomad4 ASJ
AF:
0.0312
Gnomad4 EAS
AF:
0.000772
Gnomad4 SAS
AF:
0.0565
Gnomad4 FIN
AF:
0.0339
Gnomad4 NFE
AF:
0.0502
Gnomad4 OTH
AF:
0.0572
Alfa
AF:
0.0549
Hom.:
33
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

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs73924411; hg19: chr2-27479503; API