8-264809-T-C

Variant names:

• chr8-264809-T-C
• rs888580
• ENST00000805905.1:n.444+614A>G

Variant summary

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

The ENST00000805905.1(ENSG00000288985):​n.444+614A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,138 control chromosomes in the GnomAD database, including 34,110 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 0.66 (34110 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000288985 ENST00000805905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 5 publications found

Genes affected

ENSG00000288985 (HGNC:):

ZNF596 (HGNC:27268): (zinc finger protein 596) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805905.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288985	ENST00000805905.1		n.444+614A>G		intron	N/A
	ENSG00000288985	ENST00000805906.1		n.433+614A>G		intron	N/A
	ENSG00000288985	ENST00000805907.1		n.534+614A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101030 AN: 152020 Hom.: 34065 Cov.: 34

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.665 AC: 101139 AN: 152138 Hom.: 34110 Cov.: 34 AF XY: 0.663 AC XY: 49319 AN XY: 74380

African (AFR) AF: 0.783 AC: 32496 AN: 41502

American (AMR) AF: 0.679 AC: 10388 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3120 AN: 5184

South Asian (SAS) AF: 0.595 AC: 2870 AN: 4824

European-Finnish (FIN) AF: 0.554 AC: 5852 AN: 10572

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41756 AN: 67984

Other (OTH) AF: 0.664 AC: 1400 AN: 2110

Alfa AF: 0.610 Hom.: 3878

Bravo AF: 0.679

Asia WGS AF: 0.654 AC: 2278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs888580;

hg19: chr8-214809;