rs7242481

Variant names:

• chr18-36129254-G-A
• rs7242481
• NM_012319.4:c.-150C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

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]

ENSG00000288917 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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	c.-150C>T		5_prime_UTR_variant	Exon 1 of 10	ENST00000269187.10	NP_036451.4
SLC39A6	NM_001099406.2	c.-177C>T		5_prime_UTR_variant	Exon 1 of 8		NP_001092876.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52338 AN: 152016 Hom.: 9078 Cov.: 33

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.: 0 AF XY: 0.277 AC XY: 443 AN XY: 1600

Gnomad4 AFR exome AF: 0.625

Gnomad4 AMR exome AF: 0.362

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.179

Gnomad4 SAS exome AF: 0.165

Gnomad4 FIN exome AF: 0.275

Gnomad4 NFE exome AF: 0.307

Gnomad4 OTH exome AF: 0.261

GnomAD4 genome AF: 0.344 AC: 52349 AN: 152138 Hom.: 9075 Cov.: 33 AF XY: 0.342 AC XY: 25431 AN XY: 74356

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.348

Alfa AF: 0.358 Hom.: 12094

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
DANN	Benign	0.95
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs7242481; hg19: chr18-33709217;