14-69398564-C-G

Position:

• chr14-69398564-C-G

Variant summary

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

The NM_001252151.2(SLC39A9):​c.-298C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 426,140 control chromosomes in the GnomAD database, including 7,299 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 0.19 (2816 hom., cov: 32)
  • Exomes 𝑓: 0.17 (4483 hom.)
• Consequence: SLC39A9 NM_001252151.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

Genes affected

SLC39A9 (HGNC:20182): (solute carrier family 39 member 9) Predicted to enable metal ion transmembrane transporter activity. Predicted to be involved in transmembrane transport and zinc ion transport. Predicted to be integral component of 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=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A9	NM_001252151.2	c.-298C>G		5_prime_UTR_variant	1/7
SLC39A9	NM_001252152.2	c.-400+114C>G		intron_variant
SLC39A9	XM_024449648.2	c.-259+114C>G		intron_variant
SLC39A9	XM_047431550.1	c.-259+114C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A9	ENST00000555245.5	n.179C>G		non_coding_transcript_exon_variant	1/7	2
SLC39A9	ENST00000538956.5	n.61+114C>G		intron_variant, non_coding_transcript_variant		2
SLC39A9	ENST00000556125.5	n.436+114C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28510 AN: 152032 Hom.: 2813 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0584

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.187

GnomAD4 exome AF: 0.167 AC: 45840 AN: 273992 Hom.: 4483 Cov.: 0 AF XY: 0.174 AC XY: 25252 AN XY: 144732

Gnomad4 AFR exome AF: 0.231

Gnomad4 AMR exome AF: 0.161

Gnomad4 ASJ exome AF: 0.224

Gnomad4 EAS exome AF: 0.0506

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.168

Gnomad4 NFE exome AF: 0.157

Gnomad4 OTH exome AF: 0.162

GnomAD4 genome AF: 0.187 AC: 28527 AN: 152148 Hom.: 2816 Cov.: 32 AF XY: 0.188 AC XY: 13995 AN XY: 74372

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.0587

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.185

Alfa AF: 0.178 Hom.: 320

Bravo AF: 0.186

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	4.3
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2168241; hg19: chr14-69865281;