Genetic Variant NM_012319.4:c.-150C>T (chr18-36129254-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_012319.4(SLC39A6):c.-150C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 155,164 control chromosomes in the GnomAD database, including 9,234 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 0.34 ( 9075 hom., cov: 33)

Exomes 𝑓: 0.29 ( 159 hom. )

Consequence

SLC39A6
NM_012319.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88

Publications

25 publications found

Variant links:

Genes affected

SLC39A6 (HGNC:18607): (solute carrier family 39 member 6) 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. SLC39A6 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Mar 2008]

SLC39A6 links:

ENSG00000288917 (HGNC:):

ENSG00000288917 links:

ELP2 (HGNC:18248): (elongator acetyltransferase complex subunit 2) The protein encoded by this gene is a core subunit of the elongator complex, a histone acetyltransferase complex that associates with RNA polymerase II. In addition to histone acetylation, the encoded protein effects transcriptional elongation and may help remodel chromatin. [provided by RefSeq, May 2016]

ELP2 Gene-Disease associations (from GenCC):

intellectual disability, autosomal recessive 58
Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

ELP2 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC39A6	NM_012319.4 link	c.-150C>T		5_prime_UTR_variant	Exon 1 of 10	ENST00000269187.10	NP_036451.4	Q13433-1
SLC39A6	NM_001099406.2 link	c.-177C>T		5_prime_UTR_variant	Exon 1 of 8		NP_001092876.1	Q13433-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A6	ENST00000269187.10 link	c.-150C>T		5_prime_UTR_variant	Exon 1 of 10	2	NM_012319.4	ENSP00000269187.4		Q13433-1

Frequencies

GnomAD3 genomes

AF:

0.344

AC:

52338

AN:

152016

Hom.:

9078

Cov.:

show subpopulations

Gnomad AFR

AF:

0.351

Gnomad AMI

AF:

0.287

Gnomad AMR

AF:

0.360

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.196

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.341

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.354

Gnomad OTH

AF:

0.350

GnomAD4 exome

AF:

0.290

AC:

879

AN:

3026

Hom.:

159

Cov.:

AF XY:

0.277

AC XY:

443

AN XY:

1600

show subpopulations

African (AFR)

AF:

0.625

AC:

AN:

American (AMR)

AF:

0.362

AC:

184

AN:

508

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.179

AC:

AN:

South Asian (SAS)

AF:

0.165

AC:

AN:

496

European-Finnish (FIN)

AF:

0.275

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.307

AC:

568

AN:

1848

Other (OTH)

AF:

0.261

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

110

138

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.344

AC:

52349

AN:

152138

Hom.:

9075

Cov.:

AF XY:

0.342

AC XY:

25431

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.351

AC:

14573

AN:

41542

American (AMR)

AF:

0.360

AC:

5509

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.383

AC:

1330

AN:

3470

East Asian (EAS)

AF:

0.196

AC:

1005

AN:

5136

South Asian (SAS)

AF:

0.232

AC:

1117

AN:

4824

European-Finnish (FIN)

AF:

0.341

AC:

3609

AN:

10580

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.354

AC:

24080

AN:

67960

Other (OTH)

AF:

0.348

AC:

736

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1818

3635

5453

7270

9088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.356

Hom.:

21575

Bravo

AF:

0.350

Asia WGS

AF:

0.252

AC:

881

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.4

(source)

DANN

Benign

0.95

PhyloP100

-1.9

PromoterAI

-0.074

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=300/0

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over