Variant chr3-50341515-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015896.4(ZMYND10):c.1248-30T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,614,102 control chromosomes in the GnomAD database, including 28,437 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 4251 hom., cov: 33)

Exomes 𝑓: 0.15 ( 24186 hom. )

Consequence

ZMYND10
NM_015896.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.28

Variant links:

Genes affected

ZMYND10 (HGNC:19412): (zinc finger MYND-type containing 10) This gene encodes a protein containing a MYND-type zinc finger domain that likely functions in assembly of the dynein motor. Mutations in this gene can cause primary ciliary dyskinesia. This gene is also considered a tumor suppressor gene and is often mutated, deleted, or hypermethylated and silenced in cancer cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]

ZMYND10 links:

ZMYND10-AS1 (HGNC:40890): (ZMYND10 antisense RNA 1)

ZMYND10-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 3-50341515-A-G is Benign according to our data. Variant chr3-50341515-A-G is described in ClinVar as [Benign]. Clinvar id is 1231903.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
ZMYND10	NM_015896.4 linkuse as main transcript	c.1248-30T>C	intron_variant	ENST00000231749.8
ZMYND10	NM_001308379.2 linkuse as main transcript	c.1233-30T>C	intron_variant
ZMYND10	XM_005265216.4 linkuse as main transcript	c.1011-30T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMYND10	ENST00000231749.8 linkuse as main transcript	c.1248-30T>C		intron_variant		1	NM_015896.4	P1	O75800-1
ZMYND10-AS1	ENST00000440013.1 linkuse as main transcript	n.123+287A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30644

AN:

152122

Hom.:

4241

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.349

Gnomad ASJ

AF:

0.0778

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.188

GnomAD3 exomes

AF:

0.223

AC:

56025

AN:

251414

Hom.:

10633

AF XY:

0.202

AC XY:

27433

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.260

Gnomad AMR exome

AF:

0.489

Gnomad ASJ exome

AF:

0.0783

Gnomad EAS exome

AF:

0.678

Gnomad SAS exome

AF:

0.116

Gnomad FIN exome

AF:

0.182

Gnomad NFE exome

AF:

0.115

Gnomad OTH exome

AF:

0.175

GnomAD4 exome

AF:

0.147

AC:

214665

AN:

1461862

Hom.:

24186

Cov.:

AF XY:

0.144

AC XY:

104539

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.271

Gnomad4 AMR exome

AF:

0.468

Gnomad4 ASJ exome

AF:

0.0801

Gnomad4 EAS exome

AF:

0.612

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.182

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.168

GnomAD4 genome

AF:

0.202

AC:

30708

AN:

152240

Hom.:

4251

Cov.:

AF XY:

0.208

AC XY:

15472

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.262

Gnomad4 AMR

AF:

0.349

Gnomad4 ASJ

AF:

0.0778

Gnomad4 EAS

AF:

0.665

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.179

Gnomad4 NFE

AF:

0.113

Gnomad4 OTH

AF:

0.192

Alfa

AF:

0.155

Hom.:

590

Bravo

AF:

0.223

Asia WGS

AF:

0.317

AC:

1101

AN:

3478

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	GeneDx	Nov 13, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.7

DANN

Benign

0.56

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