16-87457213-T-C

Variant names:

• chr16-87457213-T-C
• rs13334632
• NM_015144.3:c.694+2795A>G

Variant summary

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

The NM_015144.3(ZCCHC14):​c.694+2795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,118 control chromosomes in the GnomAD database, including 2,531 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 0.16 (2531 hom., cov: 32)
• Consequence: ZCCHC14 NM_015144.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 4 publications found

Genes affected

ZCCHC14 (HGNC:24134): (zinc finger CCHC-type containing 14) Predicted to enable nucleic acid binding activity; phosphatidylinositol binding activity; and zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015144.3. 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
	ZCCHC14	NM_015144.3	MANE Select	c.694+2795A>G		intron	N/A	NP_055959.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZCCHC14	ENST00000671377.2	MANE Select	c.694+2795A>G		intron	N/A	ENSP00000499622.1
	ZCCHC14	ENST00000268616.9	TSL:1	c.283+2795A>G		intron	N/A	ENSP00000268616.4
	ZCCHC14	ENST00000568020.6	TSL:1	n.313+2795A>G		intron	N/A	ENSP00000455431.2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24626 AN: 152000 Hom.: 2521 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.162 AC: 24644 AN: 152118 Hom.: 2531 Cov.: 32 AF XY: 0.170 AC XY: 12668 AN XY: 74356

African (AFR) AF: 0.119 AC: 4953 AN: 41492

American (AMR) AF: 0.296 AC: 4513 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2394 AN: 5176

South Asian (SAS) AF: 0.151 AC: 729 AN: 4828

European-Finnish (FIN) AF: 0.165 AC: 1745 AN: 10584

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9117 AN: 67990

Other (OTH) AF: 0.175 AC: 369 AN: 2110

Alfa AF: 0.140 Hom.: 876

Bravo AF: 0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.73
PhyloP100		-2.4
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: rs13334632; hg19: chr16-87490819; COSMIC: COSV107275646;