NM_020342.3:c.1217-4428G>A

Variant names:

• chr2-195702188-G-A
• rs6714748
• NM_020342.3:c.1217-4428G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020342.3(SLC39A10):​c.1217-4428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,180 control chromosomes in the GnomAD database, including 1,936 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 0.15 (1936 hom., cov: 31)
• Consequence: SLC39A10 NM_020342.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 4 publications found

Genes affected

SLC39A10 (HGNC:20861): (solute carrier family 39 member 10) 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. SLC39A10 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020342.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A10	NM_020342.3	MANE Select	c.1217-4428G>A		intron	N/A	NP_065075.1
	SLC39A10	NM_001127257.2		c.1217-4428G>A		intron	N/A	NP_001120729.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A10	ENST00000359634.10	TSL:1 MANE Select	c.1217-4428G>A		intron	N/A	ENSP00000352655.5
	SLC39A10	ENST00000409086.7	TSL:1	c.1217-4428G>A		intron	N/A	ENSP00000386766.3
	SLC39A10	ENST00000430412.5	TSL:2	n.*253-4428G>A		intron	N/A	ENSP00000394995.1

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22371 AN: 152062 Hom.: 1932 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.147 AC: 22393 AN: 152180 Hom.: 1936 Cov.: 31 AF XY: 0.143 AC XY: 10609 AN XY: 74410

African (AFR) AF: 0.229 AC: 9519 AN: 41504

American (AMR) AF: 0.113 AC: 1734 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5180

South Asian (SAS) AF: 0.0939 AC: 453 AN: 4824

European-Finnish (FIN) AF: 0.0802 AC: 849 AN: 10586

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8895 AN: 68004

Other (OTH) AF: 0.153 AC: 324 AN: 2116

Alfa AF: 0.134 Hom.: 725

Bravo AF: 0.154

Asia WGS AF: 0.0590 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6714748; hg19: chr2-196566912;