rs142613783

Variant names:

• chr3-50341826-G-A
• rs142613783
• NM_015896.4:c.1105C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-50341826-G-A
• chr3-50341826-G-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_015896.4(ZMYND10):​c.1105C>T​(p.Arg369Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00637 in 1,613,930 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R369R) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0051 (7 hom., cov: 33)
  • Exomes 𝑓: 0.0065 (49 hom.)
• Consequence: ZMYND10 NM_015896.4 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 1.04
• Publications: 15 publications found

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

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.00856331).
• BP6: Variant 3-50341826-G-A is Benign according to our data. Variant chr3-50341826-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 241067.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00508 (774/152370) while in subpopulation NFE AF = 0.00904 (615/68036). AF 95% confidence interval is 0.00845. There are 7 homozygotes in GnomAd4. There are 332 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 7 AR,AD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015896.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMYND10	NM_015896.4	MANE Select	c.1105C>T	p.Arg369Trp	missense	Exon 10 of 12	NP_056980.2
	ZMYND10	NM_001308379.2		c.1090C>T	p.Arg364Trp	missense	Exon 9 of 11	NP_001295308.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMYND10	ENST00000231749.8	TSL:1 MANE Select	c.1105C>T	p.Arg369Trp	missense	Exon 10 of 12	ENSP00000231749.3
	ZMYND10	ENST00000360165.7	TSL:1	c.1090C>T	p.Arg364Trp	missense	Exon 9 of 11	ENSP00000353289.3
	ZMYND10	ENST00000475688.1	TSL:2	n.1260C>T		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.00509 AC: 775 AN: 152252 Hom.: 7 Cov.: 33

Gnomad AFR AF: 0.00111

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00137

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00351

Gnomad FIN AF: 0.00348

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00904

Gnomad OTH AF: 0.00335

GnomAD2 exomes AF: 0.00541 AC: 1357 AN: 251050 AF XY: 0.00555

Gnomad AFR exome AF: 0.000739

Gnomad AMR exome AF: 0.00119

Gnomad ASJ exome AF: 0.0104

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00389

Gnomad NFE exome AF: 0.00857

Gnomad OTH exome AF: 0.00490

GnomAD4 exome AF: 0.00650 AC: 9499 AN: 1461560 Hom.: 49 Cov.: 32 AF XY: 0.00667 AC XY: 4850 AN XY: 727052

African (AFR) AF: 0.000747 AC: 25 AN: 33476

American (AMR) AF: 0.00121 AC: 54 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.00968 AC: 253 AN: 26132

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39696

South Asian (SAS) AF: 0.00352 AC: 304 AN: 86252

European-Finnish (FIN) AF: 0.00449 AC: 239 AN: 53232

Middle Eastern (MID) AF: 0.000867 AC: 5 AN: 5768

European-Non Finnish (NFE) AF: 0.00737 AC: 8192 AN: 1111912

Other (OTH) AF: 0.00705 AC: 426 AN: 60384

GnomAD4 genome AF: 0.00508 AC: 774 AN: 152370 Hom.: 7 Cov.: 33 AF XY: 0.00446 AC XY: 332 AN XY: 74518

African (AFR) AF: 0.00111 AC: 46 AN: 41594

American (AMR) AF: 0.00137 AC: 21 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00331 AC: 16 AN: 4834

European-Finnish (FIN) AF: 0.00348 AC: 37 AN: 10626

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00904 AC: 615 AN: 68036

Other (OTH) AF: 0.00332 AC: 7 AN: 2110

Alfa AF: 0.00751 Hom.: 21

Bravo AF: 0.00427

TwinsUK AF: 0.00701 AC: 26

ALSPAC AF: 0.00415 AC: 16

ESP6500AA AF: 0.00159 AC: 7

ESP6500EA AF: 0.00779 AC: 67

ExAC AF: 0.00568 AC: 689

Asia WGS AF: 0.000866 AC: 3 AN: 3478

EpiCase AF: 0.00720

EpiControl AF: 0.00593

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jun 11, 2025

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

See Variant Classification Assertion Criteria.

May 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ZMYND10: BP4, BS2

Primary ciliary dyskinesia Benign:1

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.20
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.48	T
Eigen	Benign	0.12
Eigen_PC	Benign	-0.016
FATHMM_MKL	Benign	0.65	D
LIST_S2	Uncertain	0.92	D
M_CAP	Benign	0.047	D
MetaRNN	Benign	0.0086	T
MetaSVM	Benign	-0.73	T
MutationAssessor	Uncertain	2.5	M
PhyloP100		1.0
PrimateAI	Benign	0.41	T
PROVEAN	Pathogenic	-5.7	D
REVEL	Benign	0.16
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0020	D
Polyphen		1.0	D
Vest4		0.60
MVP		0.15
MPC		0.41
ClinPred		0.033	T
GERP RS		2.2
Varity_R		0.29
gMVP		0.67
Mutation Taster		=96/4	polymorphism

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

Other links and lift over

dbSNP: rs142613783; hg19: chr3-50379257; COSMIC: COSV104572892; COSMIC: COSV104572892;