chr11-76487517-G-A

Variant names:

• chr11-76487517-G-A
• rs7106446
• NM_001300942.2:c.1154-8698G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001300942.2(EMSY):​c.1154-8698G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0555 in 152,238 control chromosomes in the GnomAD database, including 339 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 0.055 (339 hom., cov: 32)
• Consequence: EMSY NM_001300942.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.086 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EMSY	NM_001300942.2	c.1154-8698G>A		intron_variant	Intron 9 of 21	ENST00000695367.1	NP_001287871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMSY	ENST00000695367.1	c.1154-8698G>A		intron_variant	Intron 9 of 21		NM_001300942.2	ENSP00000511840.1

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8449 AN: 152120 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.0658

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0243

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0879

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0555 AC: 8447 AN: 152238 Hom.: 339 Cov.: 32 AF XY: 0.0523 AC XY: 3895 AN XY: 74440

African (AFR) AF: 0.0151 AC: 626 AN: 41540

American (AMR) AF: 0.0550 AC: 840 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0658 AC: 228 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.0243 AC: 117 AN: 4820

European-Finnish (FIN) AF: 0.0406 AC: 430 AN: 10586

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0879 AC: 5979 AN: 68030

Other (OTH) AF: 0.0705 AC: 149 AN: 2112

Alfa AF: 0.0767 Hom.: 330

Bravo AF: 0.0548

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.70
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

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: rs7106446; hg19: chr11-76198561;