16-87457213-T-C

Position:

• chr16-87457213-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZCCHC14	NM_015144.3	c.694+2795A>G		intron_variant		ENST00000671377.2
ZCCHC14	XM_005255858.4	c.694+2795A>G		intron_variant
ZCCHC14	XM_017023082.3	c.175+2795A>G		intron_variant
ZCCHC14	XR_243401.4	n.1480+2795A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZCCHC14	ENST00000671377.2	c.694+2795A>G		intron_variant			NM_015144.3	P1
ZCCHC14	ENST00000268616.9	c.283+2795A>G		intron_variant		1
ZCCHC14	ENST00000568020.6	c.315+2795A>G		intron_variant, NMD_transcript_variant		1

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

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.175

Alfa AF: 0.139 Hom.: 775

Bravo AF: 0.177

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.73

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: rs13334632; hg19: chr16-87490819;