18-62557961-C-T

Position:

• chr18-62557961-C-T

Variant summary

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

The NM_017742.6(ZCCHC2):​c.1409-726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 151,304 control chromosomes in the GnomAD database, including 621 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 0.061 (621 hom., cov: 32)
• Consequence: ZCCHC2 NM_017742.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

Genes affected

ZCCHC2 (HGNC:22916): (zinc finger CCHC-type containing 2) Predicted to enable nucleic acid binding activity; phosphatidylinositol binding activity; and zinc ion binding activity. Located in cytoplasm. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZCCHC2	NM_017742.6	c.1409-726C>T		intron_variant		ENST00000269499.10
ZCCHC2	NR_126534.2	n.1809-726C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZCCHC2	ENST00000269499.10	c.1409-726C>T		intron_variant		5	NM_017742.6	P1

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9193 AN: 151244 Hom.: 617 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.00801

Gnomad MID AF: 0.0325

Gnomad NFE AF: 0.0230

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0609 AC: 9212 AN: 151304 Hom.: 621 Cov.: 32 AF XY: 0.0583 AC XY: 4304 AN XY: 73838

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0144

Gnomad4 FIN AF: 0.00801

Gnomad4 NFE AF: 0.0230

Gnomad4 OTH AF: 0.0477

Alfa AF: 0.0335 Hom.: 71

Bravo AF: 0.0682

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.75

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: rs8097720; hg19: chr18-60225194;