17-16631280-G-C

Position:

• chr17-16631280-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZNF624	NM_020787.4	c.376+2582C>G		intron_variant		ENST00000311331.12	NP_065838.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF624	ENST00000311331.12	c.376+2582C>G		intron_variant		2	NM_020787.4	ENSP00000310472.7

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

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.202

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

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: rs8074464; hg19: chr17-16534594;