rs9302952

Positions:

• chr17-73068087-A-C

Variant summary

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

The NM_139177.4(SLC39A11):​c.147+16721T>G variant causes a intron change. The variant allele was found at a frequency of 0.145 in 1,458,076 control chromosomes in the GnomAD database, including 16,250 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 0.14 (1523 hom., cov: 31)
  • Exomes 𝑓: 0.15 (14727 hom.)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.80

Genes affected

SLC39A11 (HGNC:14463): (solute carrier family 39 member 11) Predicted to enable zinc ion transmembrane transporter activity. Predicted to be involved in zinc ion transmembrane transport. Predicted to be located in Golgi apparatus; nucleus; and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ATG12P1 (HGNC:21466): (autophagy related 12 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A11	NM_139177.4	c.147+16721T>G		intron_variant		ENST00000255559.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A11	ENST00000255559.8	c.147+16721T>G		intron_variant		1	NM_139177.4	P4
ATG12P1	ENST00000578331.1	n.202T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21107 AN: 151804 Hom.: 1525 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.00465

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.146 AC: 190180 AN: 1306154 Hom.: 14727 Cov.: 25 AF XY: 0.144 AC XY: 94826 AN XY: 657896

Gnomad4 AFR exome AF: 0.140

Gnomad4 AMR exome AF: 0.105

Gnomad4 ASJ exome AF: 0.0705

Gnomad4 EAS exome AF: 0.00193

Gnomad4 SAS exome AF: 0.123

Gnomad4 FIN exome AF: 0.157

Gnomad4 NFE exome AF: 0.157

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.139 AC: 21112 AN: 151922 Hom.: 1523 Cov.: 31 AF XY: 0.136 AC XY: 10110 AN XY: 74236

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.00467

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.112

Alfa AF: 0.144 Hom.: 297

Bravo AF: 0.135

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.1
DANN	Benign	0.77

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: rs9302952; hg19: chr17-71064226;