10-248225-T-C

Position:

• chr10-248225-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC107984190 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZMYND11	NM_001370100.5	c.1228-111T>C		intron_variant		ENST00000381604.9	NP_001357029.1
LOC107984190	XR_007062025.1	n.92+587A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZMYND11	ENST00000381604.9	c.1228-111T>C		intron_variant		5	NM_001370100.5	ENSP00000371017	P4

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

Gnomad4 AFR exome AF: 0.348

Gnomad4 AMR exome AF: 0.461

Gnomad4 ASJ exome AF: 0.308

Gnomad4 EAS exome AF: 0.503

Gnomad4 SAS exome AF: 0.374

Gnomad4 FIN exome AF: 0.371

Gnomad4 NFE exome AF: 0.302

Gnomad4 OTH exome AF: 0.319

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

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.313

Alfa AF: 0.318 Hom.: 2452

Bravo AF: 0.341

Asia WGS AF: 0.405 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.30

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

Other links and lift over

dbSNP: rs10903752; hg19: chr10-294165;