14-69427475-A-T

Variant names:

• chr14-69427475-A-T
• rs8016781
• NM_018375.5:c.205+3273A>T

Variant summary

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

The NM_018375.5(SLC39A9):​c.205+3273A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,060 control chromosomes in the GnomAD database, including 15,721 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 0.45 (15721 hom., cov: 32)
• Consequence: SLC39A9 NM_018375.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC39A9	NM_018375.5	c.205+3273A>T		intron_variant	Intron 2 of 6	ENST00000336643.10	NP_060845.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A9	ENST00000336643.10	c.205+3273A>T		intron_variant	Intron 2 of 6	1	NM_018375.5	ENSP00000336887.5

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68686 AN: 151942 Hom.: 15705 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.452 AC: 68746 AN: 152060 Hom.: 15721 Cov.: 32 AF XY: 0.452 AC XY: 33595 AN XY: 74324

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.455

Alfa AF: 0.322 Hom.: 808

Bravo AF: 0.438

Asia WGS AF: 0.362 AC: 1259 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.36

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: rs8016781; hg19: chr14-69894192;