8-143642893-C-T

Variant names:

• chr8-143642893-C-T
• rs4873815
• NM_001261843.2:c.-96+6748C>T

Variant summary

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

The NM_001261843.2(ZNF623):​c.-96+6748C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,918 control chromosomes in the GnomAD database, including 14,654 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 0.43 (14654 hom., cov: 31)
• Consequence: ZNF623 NM_001261843.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694
• Publications: 21 publications found

Genes affected

ZNF623 (HGNC:29084): (zinc finger protein 623) 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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001261843.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF623	NM_001261843.2	MANE Select	c.-96+6748C>T		intron	N/A	NP_001248772.1
	ZNF623	NM_001082480.2		c.-96+6478C>T		intron	N/A	NP_001075949.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF623	ENST00000526926.6	TSL:2 MANE Select	c.-96+6748C>T		intron	N/A	ENSP00000435232.1
	ZNF623	ENST00000458270.2	TSL:1	c.-96+6478C>T		intron	N/A	ENSP00000411139.2
	ZNF623	ENST00000857826.1		c.-96+6103C>T		intron	N/A	ENSP00000527885.1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64563 AN: 151800 Hom.: 14651 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.425 AC: 64607 AN: 151918 Hom.: 14654 Cov.: 31 AF XY: 0.433 AC XY: 32129 AN XY: 74232

African (AFR) AF: 0.512 AC: 21202 AN: 41404

American (AMR) AF: 0.445 AC: 6794 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3470

East Asian (EAS) AF: 0.805 AC: 4155 AN: 5164

South Asian (SAS) AF: 0.583 AC: 2807 AN: 4818

European-Finnish (FIN) AF: 0.371 AC: 3915 AN: 10552

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22941 AN: 67942

Other (OTH) AF: 0.454 AC: 958 AN: 2110

Alfa AF: 0.374 Hom.: 28898

Bravo AF: 0.440

Asia WGS AF: 0.697 AC: 2425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.4
DANN	Benign	0.89
PhyloP100		0.69
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4873815; hg19: chr8-144725063;