rs3885730

Positions:

• chr5-133026202-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001300816.3(ZCCHC10):​c.41+295C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,130 control chromosomes in the GnomAD database, including 4,063 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 0.23 (4063 hom., cov: 31)
• Consequence: ZCCHC10 NM_001300816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

Genes affected

ZCCHC10 (HGNC:25954): (zinc finger CCHC-type containing 10) Predicted to enable nucleic acid binding activity and zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ZCCHC10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZCCHC10	NM_001300816.3	c.41+295C>T		intron_variant		ENST00000509437.6	NP_001287745.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZCCHC10	ENST00000509437.6	c.41+295C>T		intron_variant		1	NM_001300816.3	ENSP00000423276.1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34517 AN: 152012 Hom.: 4060 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.227 AC: 34544 AN: 152130 Hom.: 4063 Cov.: 31 AF XY: 0.222 AC XY: 16485 AN XY: 74372

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.253

Alfa AF: 0.243 Hom.: 6092

Bravo AF: 0.229

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.8
DANN	Benign	0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3885730; hg19: chr5-132361894; COSMIC: COSV60773032;