chr17-73065795-T-C

Variant names:

• chr17-73065795-T-C
• rs903107
• NM_139177.4:c.147+19013A>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+19013A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,052 control chromosomes in the GnomAD database, including 14,374 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 0.43 (14374 hom., cov: 32)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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+19013A>G		intron	N/A	NP_631916.2
	SLC39A11	NM_001159770.2		c.147+19013A>G		intron	N/A	NP_001153242.1
	SLC39A11	NM_001352692.2		c.147+19013A>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+19013A>G		intron	N/A	ENSP00000255559.3
	SLC39A11	ENST00000542342.6	TSL:2	c.147+19013A>G		intron	N/A	ENSP00000445829.2
	SLC39A11	ENST00000579732.5	TSL:2	c.147+19013A>G		intron	N/A	ENSP00000464525.1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65107 AN: 151934 Hom.: 14360 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.0808

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.434

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.429 AC: 65167 AN: 152052 Hom.: 14374 Cov.: 32 AF XY: 0.428 AC XY: 31793 AN XY: 74298

African (AFR) AF: 0.436 AC: 18074 AN: 41462

American (AMR) AF: 0.369 AC: 5637 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1517 AN: 3466

East Asian (EAS) AF: 0.0808 AC: 419 AN: 5184

South Asian (SAS) AF: 0.379 AC: 1829 AN: 4826

European-Finnish (FIN) AF: 0.489 AC: 5169 AN: 10564

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31100 AN: 67962

Other (OTH) AF: 0.436 AC: 921 AN: 2114

Alfa AF: 0.434 Hom.: 27535

Bravo AF: 0.416

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		0.64
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: rs903107; hg19: chr17-71061934;