rs2717096

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr18-77217086-G-A
• chr18-77217086-G-C
• chr18-77217086-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000265844 (HGNC:):

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 = 0.712 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

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

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.385

Alfa AF: 0.418 Hom.: 7362

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2717096; hg19: chr18-74929042;