rs181715218

chr10-79425558-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_153367.4(ZCCHC24):c.447+7000A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00432 in 152,338 control chromosomes in the GnomAD database, including 3 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 0.0043 (3 hom., cov: 33)
• Consequence: ZCCHC24 NM_153367.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

ZCCHC24 (HGNC:26911): (zinc finger CCHC-type containing 24) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZCCHC24	NM_153367.4	c.447+7000A>G		intron_variant		ENST00000372336.4
ZCCHC24	XM_011539452.4	c.237+7000A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZCCHC24	ENST00000372336.4	c.447+7000A>G		intron_variant		1	NM_153367.4	P1
ZCCHC24	ENST00000372333.3	c.268+7000A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00433 AC: 659 AN: 152220 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.00135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00183

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.00320

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00729

Gnomad OTH AF: 0.00383

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

GnomAD4 genome AF: 0.00432 AC: 658 AN: 152338 Hom.: 3 Cov.: 33 AF XY: 0.00408 AC XY: 304 AN XY: 74504

Gnomad4 AFR AF: 0.00135

Gnomad4 AMR AF: 0.00183

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.00269

Gnomad4 FIN AF: 0.00320

Gnomad4 NFE AF: 0.00729

Gnomad4 OTH AF: 0.00379

Alfa AF: 0.00487 Hom.: 0

Bravo AF: 0.00402

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.56
Dann	Benign	0.44

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: rs181715218; hg19: chr10-81185314;