rs2586502

Positions:

• 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, non coding transcript 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: ENST00000509943.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.95

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000509943.2	n.131-237C>A		intron_variant, non_coding_transcript_variant		3

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;