ENST00000530759.1:n.297+476A>C

Variant names:

• chr11-76443802-T-G
• rs2282611
• ENST00000530759.1:n.297+476A>C

Variant summary

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

The ENST00000530759.1(EMSY-DT):​n.297+476A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,072 control chromosomes in the GnomAD database, including 5,849 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 0.27 (5849 hom., cov: 32)
• Consequence: EMSY-DT ENST00000530759.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 10 publications found

Genes affected

EMSY-DT (HGNC:55507): (EMSY divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EMSY-DT	NR_186346.1	n.403+476A>C		intron_variant	Intron 1 of 1
EMSY-DT	NR_186347.1	n.476+403A>C		intron_variant	Intron 1 of 1
EMSY-DT	NR_186348.1	n.403+476A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMSY-DT	ENST00000530759.1	n.297+476A>C		intron_variant	Intron 1 of 1	2
EMSY-DT	ENST00000572035.1	n.452+403A>C		intron_variant	Intron 1 of 1	3
EMSY-DT	ENST00000658868.2	n.404+476A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41063 AN: 151954 Hom.: 5845 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.270 AC: 41071 AN: 152072 Hom.: 5849 Cov.: 32 AF XY: 0.269 AC XY: 19985 AN XY: 74326

African (AFR) AF: 0.210 AC: 8704 AN: 41500

American (AMR) AF: 0.207 AC: 3164 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1335 AN: 3460

East Asian (EAS) AF: 0.127 AC: 659 AN: 5186

South Asian (SAS) AF: 0.227 AC: 1090 AN: 4808

European-Finnish (FIN) AF: 0.335 AC: 3546 AN: 10574

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21497 AN: 67956

Other (OTH) AF: 0.280 AC: 592 AN: 2112

Alfa AF: 0.300 Hom.: 11107

Bravo AF: 0.260

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.51
PhyloP100		0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2282611; hg19: chr11-76154846;