rs2379078

Positions:

• chr10-206753-T-C
• chr10-206753-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370100.5(ZMYND11):​c.117-3136T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,102 control chromosomes in the GnomAD database, including 6,932 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 0.29 (6932 hom., cov: 32)
• Consequence: ZMYND11 NM_001370100.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMYND11	NM_001370100.5	c.117-3136T>C		intron_variant		ENST00000381604.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMYND11	ENST00000381604.9	c.117-3136T>C		intron_variant		5	NM_001370100.5	P4

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44313 AN: 151984 Hom.: 6921 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.276

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.291 AC: 44337 AN: 152102 Hom.: 6932 Cov.: 32 AF XY: 0.297 AC XY: 22067 AN XY: 74348

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.277

Alfa AF: 0.298 Hom.: 14835

Bravo AF: 0.296

Asia WGS AF: 0.384 AC: 1330 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.28

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: rs2379078; hg19: chr10-252693;