rs1939469

chr11-76525176-A-G

Variant summary

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

The NM_001300942.2(EMSY):c.1867-1286A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,220 control chromosomes in the GnomAD database, including 1,786 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 0.14 (1786 hom., cov: 32)
• Consequence: EMSY NM_001300942.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

Genes affected

EMSY (HGNC:18071): (EMSY transcriptional repressor, BRCA2 interacting) Predicted to enable identical protein binding activity. Predicted to be involved in DNA repair; chromatin organization; and regulation of transcription, DNA-templated. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EMSY	NM_001300942.2	c.1867-1286A>G		intron_variant		ENST00000695367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EMSY	ENST00000695367.1	c.1867-1286A>G		intron_variant			NM_001300942.2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20733 AN: 152102 Hom.: 1792 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.136 AC: 20721 AN: 152220 Hom.: 1786 Cov.: 32 AF XY: 0.138 AC XY: 10261 AN XY: 74410

Gnomad4 AFR AF: 0.0387

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.135

Alfa AF: 0.157 Hom.: 2854

Bravo AF: 0.134

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.6
Dann	Benign	0.74

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: rs1939469; hg19: chr11-76236220;