Variant 2-27258793-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_003459.5(SLC30A3):c.237C>T(p.Ala79=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00882 in 1,614,208 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0079 ( 9 hom., cov: 33)

Exomes 𝑓: 0.0089 ( 89 hom. )

Consequence

SLC30A3
NM_003459.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.963

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 2-27258793-G-A is Benign according to our data. Variant chr2-27258793-G-A is described in ClinVar as [Benign]. Clinvar id is 788390.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.963 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A3	NM_003459.5 linkuse as main transcript	c.237C>T	p.Ala79=	synonymous_variant	2/8	ENST00000233535.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A3	ENST00000233535.9 linkuse as main transcript	c.237C>T	p.Ala79=	synonymous_variant	2/8	1	NM_003459.5	P1

Frequencies

GnomAD3 genomes

AF:

0.00787

AC:

1198

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00157

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00733

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.0189

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0115

Gnomad OTH

AF:

0.00525

GnomAD3 exomes

AF:

0.00807

AC:

2028

AN:

251254

Hom.:

AF XY:

0.00796

AC XY:

1082

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.00136

Gnomad AMR exome

AF:

0.00315

Gnomad ASJ exome

AF:

0.00526

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00167

Gnomad FIN exome

AF:

0.0243

Gnomad NFE exome

AF:

0.0106

Gnomad OTH exome

AF:

0.0109

GnomAD4 exome

AF:

0.00892

AC:

13034

AN:

1461868

Hom.:

Cov.:

AF XY:

0.00892

AC XY:

6487

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00304

Gnomad4 ASJ exome

AF:

0.00543

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00173

Gnomad4 FIN exome

AF:

0.0263

Gnomad4 NFE exome

AF:

0.00961

Gnomad4 OTH exome

AF:

0.00755

GnomAD4 genome

AF:

0.00787

AC:

1199

AN:

152340

Hom.:

Cov.:

AF XY:

0.00787

AC XY:

586

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00156

Gnomad4 AMR

AF:

0.00732

Gnomad4 ASJ

AF:

0.00576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.0189

Gnomad4 NFE

AF:

0.0115

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00928

Hom.:

Bravo

AF:

0.00609

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00998

EpiControl

AF:

0.00978

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over