10-17978060-G-C

Position:

• chr10-17978060-G-C

Variant summary

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

The NM_001145195.2(SLC39A12):​c.910G>C​(p.Val304Leu) 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. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V304I) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLC39A12 NM_001145195.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02

Genes affected

SLC39A12 (HGNC:20860): (solute carrier family 39 member 12) Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A12 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Aug 2008]

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=0.036914498).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC39A12	NM_001145195.2	c.910G>C	p.Val304Leu	missense_variant	5/13	ENST00000377369.7	NP_001138667.1
SLC39A12	NM_001282733.2	c.910G>C	p.Val304Leu	missense_variant	5/13		NP_001269662.1
SLC39A12	NM_152725.4	c.910G>C	p.Val304Leu	missense_variant	5/12		NP_689938.2
SLC39A12	NM_001282734.2	c.508G>C	p.Val170Leu	missense_variant	4/12		NP_001269663.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC39A12	ENST00000377369.7	c.910G>C	p.Val304Leu	missense_variant	5/13	1	NM_001145195.2	ENSP00000366586	A1
SLC39A12	ENST00000377371.3	c.910G>C	p.Val304Leu	missense_variant	5/13	1		ENSP00000366588	P4
SLC39A12	ENST00000377374.8	c.910G>C	p.Val304Leu	missense_variant	5/12	2		ENSP00000366591
SLC39A12	ENST00000539911.5	c.508G>C	p.Val170Leu	missense_variant	4/12	2		ENSP00000440445

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.69
CADD	Benign	0.0010
DANN	Benign	0.26
DEOGEN2	Benign	0.00023	.;T;.;.
Eigen	Benign	-2.0
Eigen_PC	Benign	-2.2
FATHMM_MKL	Benign	0.019	N
LIST_S2	Benign	0.096	T;T;T;T
M_CAP	Benign	0.0099	T
MetaRNN	Benign	0.037	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.41	.;N;N;N
MutationTaster	Benign	1.0	P;P;P;P
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.19	N;N;N;N
REVEL	Benign	0.059
Sift	Benign	0.30	T;T;T;T
Sift4G	Benign	0.75	T;T;T;T
Polyphen		0.0	.;B;B;B
Vest4		0.048
MutPred		0.20		.;Gain of loop (P = 0.1069);Gain of loop (P = 0.1069);Gain of loop (P = 0.1069);
MVP		0.030
MPC		0.023
ClinPred		0.43	T
GERP RS		-9.4
Varity_R		0.050
gMVP		0.17

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2478568; hg19: chr10-18266989;