rs2513511

Positions:

• chr11-76541587-A-G
• chr11-76541587-A-T

Variant summary

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

The NM_001300942.2(EMSY):​c.2603-629A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,230 control chromosomes in the GnomAD database, including 2,056 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 0.13 (2056 hom., cov: 32)
• Consequence: EMSY NM_001300942.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMSY	NM_001300942.2	c.2603-629A>G		intron_variant		ENST00000695367.1	NP_001287871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMSY	ENST00000695367.1	c.2603-629A>G		intron_variant			NM_001300942.2	ENSP00000511840

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20208 AN: 152112 Hom.: 2048 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.133 AC: 20218 AN: 152230 Hom.: 2056 Cov.: 32 AF XY: 0.139 AC XY: 10313 AN XY: 74424

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.145

Alfa AF: 0.142 Hom.: 1239

Bravo AF: 0.137

Asia WGS AF: 0.321 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.039
DANN	Benign	0.60

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: rs2513511; hg19: chr11-76252631;