rs11871756

Positions:

• chr17-72730105-C-G

Variant summary

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

The NM_139177.4(SLC39A11):​c.671+6545G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,200 control chromosomes in the GnomAD database, including 992 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 0.11 (992 hom., cov: 29)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC39A11	NM_139177.4	c.671+6545G>C		intron_variant		ENST00000255559.8	NP_631916.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC39A11	ENST00000255559.8	c.671+6545G>C		intron_variant		1	NM_139177.4	ENSP00000255559.3

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16636 AN: 152082 Hom.: 992 Cov.: 29

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.0429

Gnomad SAS AF: 0.0923

Gnomad FIN AF: 0.0450

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.109 AC: 16645 AN: 152200 Hom.: 992 Cov.: 29 AF XY: 0.106 AC XY: 7883 AN XY: 74384

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.0430

Gnomad4 SAS AF: 0.0915

Gnomad4 FIN AF: 0.0450

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.122

Alfa AF: 0.115 Hom.: 144

Bravo AF: 0.115

Asia WGS AF: 0.0720 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.68
DANN	Benign	0.23

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: rs11871756; hg19: chr17-70726244;