Variant 10-17961572-CT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001145195.2(SLC39A12):c.262-7del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00375 in 1,596,652 control chromosomes in the GnomAD database, including 177 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.020 ( 87 hom., cov: 32)

Exomes 𝑓: 0.0021 ( 90 hom. )

Consequence

SLC39A12
NM_001145195.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.793

Variant links:

Genes affected

SLC39A12 (HGNC:20860): (solute carrier family 39 member 12) Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A12 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Aug 2008]

SLC39A12 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 10-17961572-CT-C is Benign according to our data. Variant chr10-17961572-CT-C is described in ClinVar as [Benign]. Clinvar id is 770588.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SLC39A12	NM_001145195.2 linkuse as main transcript	c.262-7del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	ENST00000377369.7	NP_001138667.1
SLC39A12	NM_001282733.2 linkuse as main transcript	c.262-7del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		NP_001269662.1
SLC39A12	NM_001282734.2 linkuse as main transcript	c.-141-7del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		NP_001269663.1
SLC39A12	NM_152725.4 linkuse as main transcript	c.262-7del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		NP_689938.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
SLC39A12	ENST00000377369.7 linkuse as main transcript	c.262-7del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1	NM_001145195.2	ENSP00000366586	A1	Q504Y0-1
SLC39A12	ENST00000377371.3 linkuse as main transcript	c.262-7del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1		ENSP00000366588	P4	Q504Y0-4
SLC39A12	ENST00000377374.8 linkuse as main transcript	c.262-7del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	2		ENSP00000366591		Q504Y0-3
SLC39A12	ENST00000539911.5 linkuse as main transcript	c.-141-7del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	2		ENSP00000440445		Q504Y0-5

Frequencies

GnomAD3 genomes

AF:

0.0196

AC:

2977

AN:

152104

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0688

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00537

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.000250

Gnomad OTH

AF:

0.0139

GnomAD3 exomes

AF:

0.00528

AC:

1253

AN:

237246

Hom.:

AF XY:

0.00397

AC XY:

509

AN XY:

128184

show subpopulations

Gnomad AFR exome

AF:

0.0717

Gnomad AMR exome

AF:

0.00267

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000223

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000192

Gnomad OTH exome

AF:

0.00231

GnomAD4 exome

AF:

0.00208

AC:

3007

AN:

1444430

Hom.:

Cov.:

AF XY:

0.00182

AC XY:

1308

AN XY:

717588

show subpopulations

Gnomad4 AFR exome

AF:

0.0761

Gnomad4 AMR exome

AF:

0.00326

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000146

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000108

Gnomad4 OTH exome

AF:

0.00429

GnomAD4 genome

AF:

0.0196

AC:

2986

AN:

152222

Hom.:

Cov.:

AF XY:

0.0190

AC XY:

1412

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.0688

Gnomad4 AMR

AF:

0.00536

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000250

Gnomad4 OTH

AF:

0.0137

Alfa

AF:

0.0107

Hom.:

Bravo

AF:

0.0217

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.000382

EpiControl

AF:

0.000119

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

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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