rs11696358

Positions:

• chr20-47259646-C-G

Variant summary

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

The NM_001281775.3(ZMYND8):​c.1621+2642G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0733 in 152,134 control chromosomes in the GnomAD database, including 546 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 0.073 (546 hom., cov: 31)
• Consequence: ZMYND8 NM_001281775.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMYND8	NM_001281775.3	c.1621+2642G>C		intron_variant		ENST00000471951.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMYND8	ENST00000471951.7	c.1621+2642G>C		intron_variant		1	NM_001281775.3	A2

Frequencies

GnomAD3 genomes AF: 0.0734 AC: 11159 AN: 152016 Hom.: 548 Cov.: 31

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0221

Gnomad FIN AF: 0.0740

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.0733 AC: 11155 AN: 152134 Hom.: 546 Cov.: 31 AF XY: 0.0725 AC XY: 5393 AN XY: 74376

Gnomad4 AFR AF: 0.0194

Gnomad4 AMR AF: 0.0782

Gnomad4 ASJ AF: 0.0980

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.0740

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0825

Alfa AF: 0.0867 Hom.: 87

Bravo AF: 0.0715

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.66

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: rs11696358; hg19: chr20-45888390;