Variant rs164578 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_022902.5(SLC30A5):c.1692C>T(p.His564=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 1,611,112 control chromosomes in the GnomAD database, including 146,739 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 0.40 ( 12496 hom., cov: 30)

Exomes 𝑓: 0.43 ( 134243 hom. )

Consequence

SLC30A5
NM_022902.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.633

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP7

Synonymous conserved (PhyloP=0.633 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SLC30A5	NM_022902.5 linkuse as main transcript	c.1692C>T	p.His564=	synonymous_variant	13/16	ENST00000396591.8	NP_075053.2
SLC30A5	XM_005248569.4 linkuse as main transcript	c.1569C>T	p.His523=	synonymous_variant	12/15		XP_005248626.1
SLC30A5	XM_006714672.5 linkuse as main transcript	c.1692C>T	p.His564=	synonymous_variant	13/15		XP_006714735.1
SLC30A5	XM_017009749.2 linkuse as main transcript	c.1569C>T	p.His523=	synonymous_variant	12/14		XP_016865238.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC30A5	ENST00000396591.8 linkuse as main transcript	c.1692C>T	p.His564=	synonymous_variant	13/16	1	NM_022902.5	ENSP00000379836	P1	Q8TAD4-1
	ENST00000690195.2 linkuse as main transcript	n.683-6414G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

60884

AN:

151630

Hom.:

12494

Cov.:

show subpopulations

Gnomad AFR

AF:

0.334

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.423

Gnomad EAS

AF:

0.533

Gnomad SAS

AF:

0.420

Gnomad FIN

AF:

0.350

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.434

Gnomad OTH

AF:

0.416

GnomAD3 exomes

AF:

0.432

AC:

107427

AN:

248570

Hom.:

23426

AF XY:

0.429

AC XY:

57608

AN XY:

134316

show subpopulations

Gnomad AFR exome

AF:

0.331

Gnomad AMR exome

AF:

0.496

Gnomad ASJ exome

AF:

0.430

Gnomad EAS exome

AF:

0.539

Gnomad SAS exome

AF:

0.420

Gnomad FIN exome

AF:

0.360

Gnomad NFE exome

AF:

0.427

Gnomad OTH exome

AF:

0.434

GnomAD4 exome

AF:

0.427

AC:

623522

AN:

1459364

Hom.:

134243

Cov.:

AF XY:

0.427

AC XY:

309965

AN XY:

725918

show subpopulations

Gnomad4 AFR exome

AF:

0.329

Gnomad4 AMR exome

AF:

0.487

Gnomad4 ASJ exome

AF:

0.427

Gnomad4 EAS exome

AF:

0.511

Gnomad4 SAS exome

AF:

0.424

Gnomad4 FIN exome

AF:

0.359

Gnomad4 NFE exome

AF:

0.428

Gnomad4 OTH exome

AF:

0.435

GnomAD4 genome

AF:

0.401

AC:

60894

AN:

151748

Hom.:

12496

Cov.:

AF XY:

0.399

AC XY:

29578

AN XY:

74150

show subpopulations

Gnomad4 AFR

AF:

0.334

Gnomad4 AMR

AF:

0.426

Gnomad4 ASJ

AF:

0.423

Gnomad4 EAS

AF:

0.532

Gnomad4 SAS

AF:

0.419

Gnomad4 FIN

AF:

0.350

Gnomad4 NFE

AF:

0.434

Gnomad4 OTH

AF:

0.413

Alfa

AF:

0.426

Hom.:

22017

Bravo

AF:

0.403

Asia WGS

AF:

0.445

AC:

1548

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

5.9

DANN

Benign

0.82

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over