rs2448382

Positions:

• chr10-223755-C-T

Variant summary

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

The NM_001370100.5(ZMYND11):​c.438+2399C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,270 control chromosomes in the GnomAD database, including 65,995 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 0.93 (65995 hom., cov: 32)
• Consequence: ZMYND11 NM_001370100.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMYND11	NM_001370100.5	c.438+2399C>T		intron_variant		ENST00000381604.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMYND11	ENST00000381604.9	c.438+2399C>T		intron_variant		5	NM_001370100.5	P4

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141278 AN: 152152 Hom.: 65941 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.978

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.929 AC: 141389 AN: 152270 Hom.: 65995 Cov.: 32 AF XY: 0.930 AC XY: 69188 AN XY: 74434

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.978

Gnomad4 OTH AF: 0.936

Alfa AF: 0.949 Hom.: 8526

Bravo AF: 0.921

Asia WGS AF: 0.955 AC: 3313 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.27

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: rs2448382; hg19: chr10-269695;