ENST00000584843.1:n.330+11527G>A

Variant names:

• chr18-77217086-G-A
• rs2717096
• ENST00000584843.1:n.330+11527G>A

Variant summary

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

The ENST00000584843.1(ENSG00000265844):​n.330+11527G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,084 control chromosomes in the GnomAD database, including 13,248 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 0.41 (13248 hom., cov: 34)
• Consequence: ENSG00000265844 ENST00000584843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 4 publications found

Genes affected

ENSG00000265844 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265844	ENST00000584843.1	n.330+11527G>A		intron_variant	Intron 3 of 4	4
ENSG00000265844	ENST00000843890.1	n.539-12160G>A		intron_variant	Intron 3 of 3
ENSG00000309801	ENST00000844037.1	n.163-5527C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61799 AN: 151966 Hom.: 13239 Cov.: 34

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.407 AC: 61827 AN: 152084 Hom.: 13248 Cov.: 34 AF XY: 0.410 AC XY: 30447 AN XY: 74342

African (AFR) AF: 0.301 AC: 12495 AN: 41488

American (AMR) AF: 0.472 AC: 7210 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 935 AN: 3468

East Asian (EAS) AF: 0.731 AC: 3784 AN: 5174

South Asian (SAS) AF: 0.445 AC: 2149 AN: 4826

European-Finnish (FIN) AF: 0.432 AC: 4563 AN: 10556

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29361 AN: 67976

Other (OTH) AF: 0.385 AC: 811 AN: 2106

Alfa AF: 0.422 Hom.: 28597

Bravo AF: 0.403

Asia WGS AF: 0.527 AC: 1832 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	1.5
DANN	Benign	0.82
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2717096; hg19: chr18-74929042;