chr17-73068087-A-C

Variant names:

• chr17-73068087-A-C
• rs9302952
• NM_139177.4:c.147+16721T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139177.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A11	NM_139177.4	MANE Select	c.147+16721T>G		intron	N/A	NP_631916.2
	SLC39A11	NM_001159770.2		c.147+16721T>G		intron	N/A	NP_001153242.1
	SLC39A11	NM_001352692.2		c.147+16721T>G		intron	N/A	NP_001339621.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A11	ENST00000255559.8	TSL:1 MANE Select	c.147+16721T>G		intron	N/A	ENSP00000255559.3
	ATG12P1	ENST00000578331.1	TSL:6	n.202T>G		non_coding_transcript_exon	Exon 1 of 1
	SLC39A11	ENST00000542342.6	TSL:2	c.147+16721T>G		intron	N/A	ENSP00000445829.2

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

African (AFR) AF: 0.140 AC: 4244 AN: 30254

American (AMR) AF: 0.105 AC: 4674 AN: 44386

Ashkenazi Jewish (ASJ) AF: 0.0705 AC: 1775 AN: 25188

East Asian (EAS) AF: 0.00193 AC: 75 AN: 38918

South Asian (SAS) AF: 0.123 AC: 10232 AN: 82948

European-Finnish (FIN) AF: 0.157 AC: 8388 AN: 53360

Middle Eastern (MID) AF: 0.105 AC: 427 AN: 4076

European-Non Finnish (NFE) AF: 0.157 AC: 152967 AN: 972086

Other (OTH) AF: 0.135 AC: 7398 AN: 54938

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

African (AFR) AF: 0.141 AC: 5845 AN: 41418

American (AMR) AF: 0.115 AC: 1761 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3472

East Asian (EAS) AF: 0.00467 AC: 24 AN: 5144

South Asian (SAS) AF: 0.122 AC: 586 AN: 4794

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10576

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10570 AN: 67948

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.144 Hom.: 307

Bravo AF: 0.135

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.1
DANN	Benign	0.77
PhyloP100		4.8
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: rs9302952; hg19: chr17-71064226;