dbSNP rs1153831: SLC30A4:c.*4913C>T (chr15-45480250-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_013309.6(SLC30A4):c.*4913C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,100 control chromosomes in the GnomAD database, including 4,724 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 0.21 ( 4724 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SLC30A4
NM_013309.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

Publications

8 publications found

Variant links:

Genes affected

SLC30A4 (HGNC:11015): (solute carrier family 30 member 4) Zinc is the second most abundant trace metal in the human body. It is an essential element, serving both a structural role, as in the formation of zinc fingers in DNA-binding proteins, and a catalytic role in metalloenzymes, such as pancreatic carboxypeptidases (e.g., MIM 114852), alkaline phosphatases (e.g., MIM 171760), various dehydrogenases, and superoxide dismutases (e.g., MIM 147450). SLC30A4, or ZNT4, belongs to the ZNT family of zinc transporters. ZNTs are involved in transporting zinc out of the cytoplasm and have similar structures, consisting of 6 transmembrane domains and a histidine-rich cytoplasmic loop (Huang and Gitschier, 1997 [PubMed 9354792]).[supplied by OMIM, Mar 2008]

SLC30A4 links:

SLC30A4-AS1 (HGNC:56661): (SLC30A4 antisense RNA 1)

SLC30A4-AS1 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLC30A4	NM_013309.6 link	c.*4913C>T	3_prime_UTR_variant	Exon 8 of 8	ENST00000261867.5	NP_037441.2	O14863
SLC30A4-AS1	XR_007064610.1 link	n.4395G>A	non_coding_transcript_exon_variant	Exon 4 of 4
SLC30A4	XM_017022560.3 link	c.*4913C>T	3_prime_UTR_variant	Exon 7 of 7		XP_016878049.1	O14863
SLC30A4-AS1	XR_007064611.1 link	n.1913+3698G>A	intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC30A4	ENST00000261867.5 link	c.*4913C>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_013309.6	ENSP00000261867.3		O14863

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

31304

AN:

151982

Hom.:

4705

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.147

Gnomad FIN

AF:

0.0803

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.194

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.206

AC:

31365

AN:

152100

Hom.:

4724

Cov.:

AF XY:

0.203

AC XY:

15108

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.431

AC:

17845

AN:

41444

American (AMR)

AF:

0.149

AC:

2277

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

599

AN:

3468

East Asian (EAS)

AF:

0.119

AC:

618

AN:

5178

South Asian (SAS)

AF:

0.147

AC:

708

AN:

4826

European-Finnish (FIN)

AF:

0.0803

AC:

851

AN:

10602

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.116

AC:

7861

AN:

67994

Other (OTH)

AF:

0.192

AC:

405

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1138

2276

3415

4553

5691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

314

628

942

1256

1570

<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:

0.139

Hom.:

3379

Bravo

AF:

0.221

Asia WGS

AF:

0.143

AC:

500

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

0.017

(source)

DANN

Benign

0.25

PhyloP100

-1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over