rs10903752

Variant names:

• chr10-248225-T-C
• rs10903752
• NM_001370100.5:c.1228-111T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-248225-T-C
• chr10-248225-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370100.5(ZMYND11):​c.1228-111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 1,377,496 control chromosomes in the GnomAD database, including 72,952 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 0.33 (8686 hom., cov: 32)
  • Exomes 𝑓: 0.32 (64266 hom.)
• Consequence: ZMYND11 NM_001370100.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 3 publications found

Genes affected

ZMYND11 (HGNC:16966): (zinc finger MYND-type containing 11) The protein encoded by this gene was first identified by its ability to bind the adenovirus E1A protein. The protein localizes to the nucleus. It functions as a transcriptional repressor, and expression of E1A inhibits this repression. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ZMYND11 Gene-Disease associations (from GenCC):

• syndromic complex neurodevelopmental disorder

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• intellectual disability, autosomal dominant 30

  Inheritance: AD Classification: STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• autosomal dominant non-syndromic intellectual disability

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

LOC107984190 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370100.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMYND11	NM_001370100.5	MANE Select	c.1228-111T>C		intron	N/A	NP_001357029.1	Q15326-1
	ZMYND11	NM_001370097.3		c.1228-111T>C		intron	N/A	NP_001357026.1	Q15326-1
	ZMYND11	NM_001370098.2		c.1228-111T>C		intron	N/A	NP_001357027.1	Q15326-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMYND11	ENST00000381604.9	TSL:5 MANE Select	c.1228-111T>C		intron	N/A	ENSP00000371017.6	Q15326-1
	ZMYND11	ENST00000397962.8	TSL:1	c.1228-111T>C		intron	N/A	ENSP00000381053.3	Q15326-1
	ZMYND11	ENST00000558098.4	TSL:1	c.1228-111T>C		intron	N/A	ENSP00000452959.1	Q15326-3

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50420 AN: 151964 Hom.: 8652 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.313

GnomAD4 exome AF: 0.319 AC: 391133 AN: 1225416 Hom.: 64266 AF XY: 0.320 AC XY: 193772 AN XY: 604658

African (AFR) AF: 0.348 AC: 9449 AN: 27118

American (AMR) AF: 0.461 AC: 12360 AN: 26828

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 5811 AN: 18844

East Asian (EAS) AF: 0.503 AC: 18802 AN: 37400

South Asian (SAS) AF: 0.374 AC: 23605 AN: 63186

European-Finnish (FIN) AF: 0.371 AC: 17878 AN: 48250

Middle Eastern (MID) AF: 0.225 AC: 989 AN: 4394

European-Non Finnish (NFE) AF: 0.302 AC: 285884 AN: 948048

Other (OTH) AF: 0.319 AC: 16355 AN: 51348

GnomAD4 genome AF: 0.332 AC: 50496 AN: 152080 Hom.: 8686 Cov.: 32 AF XY: 0.337 AC XY: 25032 AN XY: 74330

African (AFR) AF: 0.349 AC: 14460 AN: 41446

American (AMR) AF: 0.377 AC: 5768 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3466

East Asian (EAS) AF: 0.478 AC: 2469 AN: 5170

South Asian (SAS) AF: 0.382 AC: 1845 AN: 4824

European-Finnish (FIN) AF: 0.360 AC: 3807 AN: 10566

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20140 AN: 67998

Other (OTH) AF: 0.313 AC: 662 AN: 2114

Alfa AF: 0.318 Hom.: 2754

Bravo AF: 0.341

Asia WGS AF: 0.405 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.30
PhyloP100		0.53
Mutation Taster		=98/2	polymorphism (auto)

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: rs10903752; hg19: chr10-294165;