rs11051

Variant names:

• chr4-42087160-G-A
• rs11051
• NM_006345.4:c.*1034G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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]

SLC30A9 Gene-Disease associations (from GenCC):

• psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), PanelApp Australia, ClinGen, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006345.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC30A9	NM_006345.4	MANE Select	c.*1034G>A		3_prime_UTR	Exon 18 of 18	NP_006336.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC30A9	ENST00000264451.12	TSL:1 MANE Select	c.*1034G>A		3_prime_UTR	Exon 18 of 18	ENSP00000264451.6	Q6PML9
	SLC30A9	ENST00000866307.1		c.*1034G>A		3_prime_UTR	Exon 18 of 18	ENSP00000536366.1
	SLC30A9	ENST00000962779.1		c.*1034G>A		3_prime_UTR	Exon 18 of 18	ENSP00000632838.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.152 AC: 6293 AN: 41430

American (AMR) AF: 0.734 AC: 11214 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2490 AN: 3468

East Asian (EAS) AF: 0.955 AC: 4946 AN: 5180

South Asian (SAS) AF: 0.772 AC: 3718 AN: 4814

European-Finnish (FIN) AF: 0.798 AC: 8419 AN: 10550

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50914 AN: 67968

Other (OTH) AF: 0.625 AC: 1319 AN: 2110

Alfa AF: 0.705 Hom.: 152770

Bravo AF: 0.571

Asia WGS AF: 0.819 AC: 2844 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.9
DANN	Benign	0.73
PhyloP100		-0.014
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11051; hg19: chr4-42089177;