10-209870-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The NM_001370100.5(ZMYND11):c.117-19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000487 in 1,574,400 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00045 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00049 (1 hom.)
• Consequence: ZMYND11 NM_001370100.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.32

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 10-209870-G-A is Benign according to our data. Variant chr10-209870-G-A is described in ClinVar as [Benign]. Clinvar id is 1971215.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000454 (69/152062) while in subpopulation SAS AF= 0.000832 (4/4806). AF 95% confidence interval is 0.000599. There are 0 homozygotes in gnomad4. There are 30 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd at 69 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMYND11	NM_001370100.5	c.117-19G>A		intron_variant		ENST00000381604.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMYND11	ENST00000381604.9	c.117-19G>A		intron_variant		5	NM_001370100.5	P4

Frequencies

GnomAD3 genomes AF: 0.000454 AC: 69 AN: 151944 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000967

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000832

Gnomad FIN AF: 0.0000950

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000765

Gnomad OTH AF: 0.000958

GnomAD3 exomes AF: 0.000492 AC: 113 AN: 229578 Hom.: 1 AF XY: 0.000563 AC XY: 70 AN XY: 124286

Gnomad AFR exome AF: 0.000126

Gnomad AMR exome AF: 0.000325

Gnomad ASJ exome AF: 0.000719

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000798

Gnomad FIN exome AF: 0.0000476

Gnomad NFE exome AF: 0.000670

Gnomad OTH exome AF: 0.000365

GnomAD4 exome AF: 0.000490 AC: 697 AN: 1422338 Hom.: 1 Cov.: 30 AF XY: 0.000503 AC XY: 354 AN XY: 703650

Gnomad4 AFR exome AF: 0.0000626

Gnomad4 AMR exome AF: 0.000211

Gnomad4 ASJ exome AF: 0.000491

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00126

Gnomad4 FIN exome AF: 0.0000189

Gnomad4 NFE exome AF: 0.000469

Gnomad4 OTH exome AF: 0.000632

GnomAD4 genome AF: 0.000454 AC: 69 AN: 152062 Hom.: 0 Cov.: 33 AF XY: 0.000404 AC XY: 30 AN XY: 74296

Gnomad4 AFR AF: 0.0000964

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000832

Gnomad4 FIN AF: 0.0000950

Gnomad4 NFE AF: 0.000765

Gnomad4 OTH AF: 0.000948

Alfa AF: 0.000538 Hom.: 0

Bravo AF: 0.000400

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 25, 2023

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	8.1
Dann	Benign	0.56

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: rs200268452; hg19: chr10-255810;