rs888580

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-264809-T-C
• chr8-264809-T-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927566	XR_245320.4	n.392+614A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288985	ENST00000805905.1	n.444+614A>G		intron_variant	Intron 3 of 6
ENSG00000288985	ENST00000805906.1	n.433+614A>G		intron_variant	Intron 3 of 6
ENSG00000288985	ENST00000805907.1	n.534+614A>G		intron_variant	Intron 4 of 7

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 v4.3

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

Other links and lift over

dbSNP: rs888580; hg19: chr8-214809;