NM_139177.4:c.671+36686G>A

Variant names:

• chr17-72699964-C-T
• rs8066857
• NM_139177.4:c.671+36686G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139177.4(SLC39A11):​c.671+36686G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 149,344 control chromosomes in the GnomAD database, including 5,705 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 0.25 (5705 hom., cov: 32)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 11 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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.671+36686G>A		intron	N/A	NP_631916.2
	SLC39A11	NM_001159770.2		c.692+36686G>A		intron	N/A	NP_001153242.1
	SLC39A11	NM_001352692.2		c.692+36686G>A		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.671+36686G>A		intron	N/A	ENSP00000255559.3
	SLC39A11	ENST00000542342.6	TSL:2	c.692+36686G>A		intron	N/A	ENSP00000445829.2
	SLC39A11	ENST00000582769.5	TSL:5	c.419+36686G>A		intron	N/A	ENSP00000463467.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38041 AN: 149228 Hom.: 5695 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.0741

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.255 AC: 38052 AN: 149344 Hom.: 5705 Cov.: 32 AF XY: 0.259 AC XY: 18903 AN XY: 73004

African (AFR) AF: 0.367 AC: 14997 AN: 40916

American (AMR) AF: 0.187 AC: 2811 AN: 15018

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 816 AN: 3388

East Asian (EAS) AF: 0.355 AC: 1813 AN: 5110

South Asian (SAS) AF: 0.343 AC: 1639 AN: 4776

European-Finnish (FIN) AF: 0.274 AC: 2827 AN: 10318

Middle Eastern (MID) AF: 0.213 AC: 60 AN: 282

European-Non Finnish (NFE) AF: 0.188 AC: 12501 AN: 66564

Other (OTH) AF: 0.252 AC: 521 AN: 2068

Alfa AF: 0.218 Hom.: 15850

Bravo AF: 0.260

Asia WGS AF: 0.353 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.57
PhyloP100		0.044
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: rs8066857; hg19: chr17-70696103;