NM_020787.4:c.376+2582C>G

Variant names:

• chr17-16631280-G-C
• rs8074464
• NM_020787.4:c.376+2582C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020787.4(ZNF624):​c.376+2582C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,940 control chromosomes in the GnomAD database, including 4,556 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 (4556 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZNF624 NM_020787.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 3 publications found

Genes affected

ZNF624 (HGNC:29254): (zinc finger protein 624) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF624	NM_020787.4	c.376+2582C>G		intron_variant	Intron 5 of 5	ENST00000311331.12	NP_065838.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF624	ENST00000311331.12	c.376+2582C>G		intron_variant	Intron 5 of 5	2	NM_020787.4	ENSP00000310472.7
ZNF624	ENST00000579983.1	n.*64C>G		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35210 AN: 151822 Hom.: 4550 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.232 AC: 35248 AN: 151940 Hom.: 4556 Cov.: 32 AF XY: 0.232 AC XY: 17225 AN XY: 74266

African (AFR) AF: 0.336 AC: 13903 AN: 41416

American (AMR) AF: 0.193 AC: 2947 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3462

East Asian (EAS) AF: 0.355 AC: 1839 AN: 5176

South Asian (SAS) AF: 0.152 AC: 732 AN: 4812

European-Finnish (FIN) AF: 0.225 AC: 2375 AN: 10538

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12103 AN: 67956

Other (OTH) AF: 0.202 AC: 425 AN: 2100

Alfa AF: 0.0844 Hom.: 95

Bravo AF: 0.239

Asia WGS AF: 0.216 AC: 748 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.5
DANN	Benign	0.83
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

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: rs8074464; hg19: chr17-16534594;