Variant 9-137583064-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_138462.3(ZMYND19):c.459C>T(p.Asn153=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0024 in 1,614,164 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0044 ( 10 hom., cov: 33)

Exomes 𝑓: 0.0022 ( 57 hom. )

Consequence

ZMYND19
NM_138462.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.697

Variant links:

Genes affected

ZMYND19 (HGNC:21146): (zinc finger MYND-type containing 19) ZMYND19 is a MYND zinc finger domain-containing protein that binds to the C terminus of melanin-concentrating hormone receptor-1 (MCHR1; MIM 601751) (Bachner et al., 2002 [PubMed 12208518]), and to the N termini of alpha-tubulin (TUBA1; MIM 191110), and beta-tubulin (TUBB; MIM 191130) (Francke et al., 2005 [PubMed 16039987]).[supplied by OMIM, Mar 2008]

ZMYND19 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 9-137583064-G-A is Benign according to our data. Variant chr9-137583064-G-A is described in ClinVar as [Benign]. Clinvar id is 782710.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.697 with no splicing effect.

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00439 (668/152296) while in subpopulation AMR AF= 0.0318 (487/15296). AF 95% confidence interval is 0.0295. There are 10 homozygotes in gnomad4. There are 373 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZMYND19	NM_138462.3 linkuse as main transcript	c.459C>T	p.Asn153=	synonymous_variant	5/6	ENST00000298585.3	NP_612471.1
ZMYND19	XM_005266052.5 linkuse as main transcript	c.642C>T	p.Asn214=	synonymous_variant	5/6		XP_005266109.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZMYND19	ENST00000298585.3 linkuse as main transcript	c.459C>T	p.Asn153=	synonymous_variant	5/6	1	NM_138462.3	ENSP00000298585	P1

Frequencies

GnomAD3 genomes

AF:

0.00438

AC:

666

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000796

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0317

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.00273

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00125

Gnomad OTH

AF:

0.00812

GnomAD3 exomes

AF:

0.00548

AC:

1377

AN:

251478

Hom.:

AF XY:

0.00472

AC XY:

642

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.000615

Gnomad AMR exome

AF:

0.0307

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00314

Gnomad FIN exome

AF:

0.00212

Gnomad NFE exome

AF:

0.00114

Gnomad OTH exome

AF:

0.00521

GnomAD4 exome

AF:

0.00219

AC:

3208

AN:

1461868

Hom.:

Cov.:

AF XY:

0.00220

AC XY:

1603

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.000388

Gnomad4 AMR exome

AF:

0.0339

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00336

Gnomad4 FIN exome

AF:

0.00170

Gnomad4 NFE exome

AF:

0.00103

Gnomad4 OTH exome

AF:

0.00238

GnomAD4 genome

AF:

0.00439

AC:

668

AN:

152296

Hom.:

Cov.:

AF XY:

0.00501

AC XY:

373

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.000794

Gnomad4 AMR

AF:

0.0318

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.00273

Gnomad4 NFE

AF:

0.00125

Gnomad4 OTH

AF:

0.00803

Alfa

AF:

0.00168

Hom.:

Bravo

AF:

0.00713

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00142

EpiControl

AF:

0.00124

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

2.6

DANN

Benign

0.80

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over