rs2586502

Variant names:

• chr17-50211709-C-A
• rs2586502
• ENST00000509943.2:n.131-237C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-50211709-C-A
• chr17-50211709-C-G

Variant summary

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

The ENST00000509943.2(ENSG00000249406):​n.131-237C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.864 in 152,126 control chromosomes in the GnomAD database, including 57,579 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 0.86 (57579 hom., cov: 31)
• Consequence: ENSG00000249406 ENST00000509943.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.95

Genes affected

ENSG00000249406 (HGNC:52795): (long intergenic non-protein coding RNA 1969)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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
ENSG00000249406	ENST00000509943.2	n.131-237C>A		intron_variant	Intron 2 of 6	3
ENSG00000249406	ENST00000514468.2	n.384+907C>A		intron_variant	Intron 3 of 7	3
ENSG00000249406	ENST00000650459.1	n.252-2126C>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131422 AN: 152008 Hom.: 57549 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.864 AC: 131511 AN: 152126 Hom.: 57579 Cov.: 31 AF XY: 0.869 AC XY: 64654 AN XY: 74380

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.893

Alfa AF: 0.912 Hom.: 85577

Bravo AF: 0.858

Asia WGS AF: 0.948 AC: 3296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2586502; hg19: chr17-48289070;