NM_153367.4:c.447+7000A>G

Variant names:

• chr10-79425558-T-C
• rs181715218
• NM_153367.4:c.447+7000A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd4 at 3 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153367.4. 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
	ZCCHC24	NM_153367.4	MANE Select	c.447+7000A>G		intron	N/A	NP_699198.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZCCHC24	ENST00000372336.4	TSL:1 MANE Select	c.447+7000A>G		intron	N/A	ENSP00000361411.3
	ZCCHC24	ENST00000372333.3	TSL:2	c.268+7000A>G		intron	N/A	ENSP00000361408.3

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

African (AFR) AF: 0.00135 AC: 56 AN: 41578

American (AMR) AF: 0.00183 AC: 28 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00432 AC: 15 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.00269 AC: 13 AN: 4828

European-Finnish (FIN) AF: 0.00320 AC: 34 AN: 10624

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00729 AC: 496 AN: 68026

Other (OTH) AF: 0.00379 AC: 8 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.44
PhyloP100		-0.096
Mutation Taster		=100/0	polymorphism

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: rs181715218; hg19: chr10-81185314;