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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000509943.2(TILAM):​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: TILAM ENST00000509943.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.95
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509943.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TILAM	ENST00000509943.2	TSL:3	n.131-237C>A		intron	N/A
	TILAM	ENST00000514468.3	TSL:3	n.384+907C>A		intron	N/A
	TILAM	ENST00000650459.1		n.252-2126C>A		intron	N/A

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

African (AFR) AF: 0.710 AC: 29431 AN: 41446

American (AMR) AF: 0.919 AC: 14042 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3085 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5163 AN: 5174

South Asian (SAS) AF: 0.928 AC: 4473 AN: 4822

European-Finnish (FIN) AF: 0.934 AC: 9904 AN: 10608

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62416 AN: 68010

Other (OTH) AF: 0.893 AC: 1885 AN: 2112

Alfa AF: 0.894 Hom.: 129396

Bravo AF: 0.858

Asia WGS AF: 0.948 AC: 3296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.27
PhyloP100		-6.0

Splicing

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

Other links and lift over

dbSNP: rs2586502; hg19: chr17-48289070;