rs2282611

Positions:

• chr11-76443802-T-G

Variant summary

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

The ENST00000658868.1(EMSY-DT):​n.396+476A>C variant causes a intron, non coding transcript 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 ENST00000658868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553

Genes affected

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

LOC124902718 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124902718	XR_007062786.1	n.403+476A>C		intron_variant, non_coding_transcript_variant
LOC124902718	XR_007062787.1	n.476+403A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EMSY-DT	ENST00000658868.1	n.396+476A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.280

Alfa AF: 0.304 Hom.: 7761

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2282611; hg19: chr11-76154846;