chr20-47225746-T-C

Position:

• chr20-47225746-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001281775.3(ZMYND8):​c.3017-1190A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,402 control chromosomes in the GnomAD database, including 8,851 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 0.29 (8851 hom., cov: 28)
• Consequence: ZMYND8 NM_001281775.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

Genes affected

ZMYND8 (HGNC:9397): (zinc finger MYND-type containing 8) The protein encoded by this gene is a receptor for activated C-kinase (RACK) protein. The encoded protein has been shown to bind in vitro to activated protein kinase C beta I. In addition, this protein is a cutaneous T-cell lymphoma-associated antigen. Finally, the protein contains a bromodomain and two zinc fingers, and is thought to be a transcriptional regulator. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMYND8	NM_001281775.3	c.3017-1190A>G		intron_variant		ENST00000471951.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMYND8	ENST00000471951.7	c.3017-1190A>G		intron_variant		1	NM_001281775.3	A2

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44360 AN: 151286 Hom.: 8832 Cov.: 28

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.293 AC: 44431 AN: 151402 Hom.: 8851 Cov.: 28 AF XY: 0.293 AC XY: 21657 AN XY: 73994

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.266

Alfa AF: 0.250 Hom.: 1432

Bravo AF: 0.308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3091566; hg19: chr20-45854487;