rs11696358

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0770
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
ZMYND8NM_001281775.3 linkuse as main transcriptc.1621+2642G>C intron_variant ENST00000471951.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZMYND8ENST00000471951.7 linkuse as main transcriptc.1621+2642G>C intron_variant 1 NM_001281775.3 A2Q9ULU4-7

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11696358; hg19: chr20-45888390; API