Variant 5-69100936-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022902.5(SLC30A5):c.206+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0054 in 1,469,760 control chromosomes in the GnomAD database, including 323 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.027 ( 165 hom., cov: 30)

Exomes 𝑓: 0.0030 ( 158 hom. )

Consequence

SLC30A5
NM_022902.5 splice_region, intron

Scores

Splicing: ADA: 0.0002949

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.384

Variant links:

Genes affected

SLC30A5 (HGNC:19089): (solute carrier family 30 member 5) This gene encodes a member of the SLC30A/ZnT family of zinc transporter proteins. ZnT proteins mediate both cellular zinc efflux and zinc sequestration into membrane-bound organelles. The encoded protein plays a role in the early secretory pathway as a heterodimer with zinc transporter 6, and may also regulate zinc sequestration into secretory granules of pancreatic beta cells. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 19. [provided by RefSeq, Oct 2011]

SLC30A5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 5-69100936-G-A is Benign according to our data. Variant chr5-69100936-G-A is described in ClinVar as [Benign]. Clinvar id is 778191.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC30A5	NM_022902.5 linkuse as main transcript	c.206+7G>A		splice_region_variant, intron_variant		ENST00000396591.8	NP_075053.2	Q8TAD4-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
SLC30A5	ENST00000396591.8 linkuse as main transcript	c.206+7G>A	splice_region_variant, intron_variant	1	NM_022902.5	ENSP00000379836.3	Q8TAD4-1
SLC30A5	ENST00000380860.8 linkuse as main transcript	c.206+7G>A	splice_region_variant, intron_variant	1		ENSP00000370241.4	Q8TAD4-3
SLC30A5	ENST00000502979.1 linkuse as main transcript	c.84-2126G>A	intron_variant	1		ENSP00000421251.1	Q8TAD4-4
SLC30A5	ENST00000504103.5 linkuse as main transcript	c.84-2126G>A	intron_variant	3		ENSP00000426751.1	D6REM2

Frequencies

GnomAD3 genomes

AF:

0.0273

AC:

3879

AN:

141950

Hom.:

164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0899

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0113

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000917

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00362

Gnomad NFE

AF:

0.000602

Gnomad OTH

AF:

0.0244

GnomAD3 exomes

AF:

0.00778

AC:

1607

AN:

206510

Hom.:

AF XY:

0.00557

AC XY:

630

AN XY:

113034

show subpopulations

Gnomad AFR exome

AF:

0.0911

Gnomad AMR exome

AF:

0.00666

Gnomad ASJ exome

AF:

0.000136

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000171

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000728

Gnomad OTH exome

AF:

0.00382

GnomAD4 exome

AF:

0.00304

AC:

4040

AN:

1327688

Hom.:

158

Cov.:

AF XY:

0.00265

AC XY:

1748

AN XY:

659408

show subpopulations

Gnomad4 AFR exome

AF:

0.0978

Gnomad4 AMR exome

AF:

0.00733

Gnomad4 ASJ exome

AF:

0.000136

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000273

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000368

Gnomad4 OTH exome

AF:

0.00748

GnomAD4 genome

AF:

0.0274

AC:

3890

AN:

142072

Hom.:

165

Cov.:

AF XY:

0.0262

AC XY:

1813

AN XY:

69306

show subpopulations

Gnomad4 AFR

AF:

0.0899

Gnomad4 AMR

AF:

0.0112

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000917

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000602

Gnomad4 OTH

AF:

0.0241

Alfa

AF:

0.00939

Hom.:

Bravo

AF:

0.0297

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 30, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

1.6

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00029

dbscSNV1_RF

Benign

0.0060

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.

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