14-21000121-A-T

Variant names:

• chr14-21000121-A-T
• NM_014579.4:c.252A>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014579.4(SLC39A2):​c.252A>T​(p.Arg84Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC39A2 NM_014579.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.197

Genes affected

SLC39A2 (HGNC:17127): (solute carrier family 39 member 2) This gene encodes a member of the ZIP family of metal ion transporters. The encoded protein functions as a zinc transporter. Mutations in this gene may be associated with susceptibility to carotid artery disease. Multiple transcript variants have been described. [provided by RefSeq, Mar 2010]

ENSG00000258471 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03699702).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC39A2	NM_014579.4	c.252A>T	p.Arg84Ser	missense_variant	Exon 3 of 4	ENST00000298681.5	NP_055394.2
SLC39A2	NM_001256588.2	c.247A>T	p.Ile83Phe	missense_variant, splice_region_variant	Exon 3 of 4		NP_001243517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A2	ENST00000298681.5	c.252A>T	p.Arg84Ser	missense_variant	Exon 3 of 4	1	NM_014579.4	ENSP00000298681.4
SLC39A2	ENST00000554422.5	c.247A>T	p.Ile83Phe	missense_variant, splice_region_variant	Exon 3 of 4	1		ENSP00000452568.1
ENSG00000258471	ENST00000647921.1	n.398-291T>A		intron_variant	Intron 1 of 4
SLC39A2	ENST00000554128.1	n.*88A>T		downstream_gene_variant		4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Dec 19, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.252A>T (p.R84S) alteration is located in exon 3 (coding exon 3) of the SLC39A2 gene. This alteration results from a A to T substitution at nucleotide position 252, causing the arginine (R) at amino acid position 84 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	7.7
DANN	Benign	0.70
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.18	N
LIST_S2	Benign	0.23	T
M_CAP	Benign	0.0049	T
MetaRNN	Benign	0.037	T
MetaSVM	Benign	-1.0	T
PROVEAN	Benign	-0.75	N
REVEL	Benign	0.073
Sift	Benign	0.057	T
Sift4G	Benign	0.30	T
Vest4		0.13
MutPred		0.14		Loss of MoRF binding (P = 0.0924);
MVP		0.030
ClinPred		0.11	T
GERP RS		-1.7

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-21468280;