rs11051

Positions:

• chr4-42087160-G-A
• chr4-42087160-G-C
• chr4-42087160-G-T

Variant summary

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

The NM_006345.4(SLC30A9):​c.*1034G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,004 control chromosomes in the GnomAD database, including 32,710 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 0.59 (32709 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: SLC30A9 NM_006345.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

SLC30A9 (HGNC:1329): (solute carrier family 30 member 9) Predicted to enable nuclear receptor coactivator activity. Involved in cellular zinc ion homeostasis and zinc ion transport. Located in several cellular components, including cytoplasmic vesicle; cytoskeleton; and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC30A9	NM_006345.4	c.*1034G>A		3_prime_UTR_variant	18/18	ENST00000264451.12	NP_006336.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC30A9	ENST00000264451.12	c.*1034G>A		3_prime_UTR_variant	18/18	1	NM_006345.4	ENSP00000264451	P1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90311 AN: 151884 Hom.: 32699 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.621

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.594 AC: 90324 AN: 152002 Hom.: 32709 Cov.: 32 AF XY: 0.604 AC XY: 44841 AN XY: 74272

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.625

Alfa AF: 0.728 Hom.: 68519

Bravo AF: 0.571

Asia WGS AF: 0.819 AC: 2844 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.9
DANN	Benign	0.73
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: rs11051; hg19: chr4-42089177;