8-117144111-G-C

Variant summary

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

The NM_173851.3(SLC30A8):​c.72-2843G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,080 control chromosomes in the GnomAD database, including 2,342 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 0.15 ( 2342 hom., cov: 32)

Consequence

SLC30A8
NM_173851.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.280
Variant links:
Genes affected
SLC30A8 (HGNC:20303): (solute carrier family 30 member 8) The protein encoded by this gene is a zinc efflux transporter involved in the accumulation of zinc in intracellular vesicles. This gene is expressed at a high level only in the pancreas, particularly in islets of Langerhans. The encoded protein colocalizes with insulin in the secretory pathway granules of the insulin-secreting INS-1 cells. Allelic variants of this gene exist that confer susceptibility to diabetes mellitus, noninsulin-dependent (NIDDM). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]

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=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC30A8NM_173851.3 linkc.72-2843G>C intron_variant ENST00000456015.7 NP_776250.2 Q8IWU4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC30A8ENST00000456015.7 linkc.72-2843G>C intron_variant 1 NM_173851.3 ENSP00000415011.2 Q8IWU4-1

Frequencies

GnomAD3 genomes
AF:
0.152
AC:
23101
AN:
151962
Hom.:
2343
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0337
Gnomad AMI
AF:
0.412
Gnomad AMR
AF:
0.103
Gnomad ASJ
AF:
0.286
Gnomad EAS
AF:
0.211
Gnomad SAS
AF:
0.328
Gnomad FIN
AF:
0.192
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.200
Gnomad OTH
AF:
0.175
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.152
AC:
23090
AN:
152080
Hom.:
2342
Cov.:
32
AF XY:
0.154
AC XY:
11453
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.0337
Gnomad4 AMR
AF:
0.103
Gnomad4 ASJ
AF:
0.286
Gnomad4 EAS
AF:
0.210
Gnomad4 SAS
AF:
0.328
Gnomad4 FIN
AF:
0.192
Gnomad4 NFE
AF:
0.200
Gnomad4 OTH
AF:
0.177
Alfa
AF:
0.104
Hom.:
179
Bravo
AF:
0.138
Asia WGS
AF:
0.224
AC:
782
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
1.5
DANN
Benign
0.53

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

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

Other links and lift over

dbSNP: rs17738231; hg19: chr8-118156350; API