Genetic Variant TILAM:n.59+3361delA (chr17-50203294-GA-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000509943.2(TILAM):n.59+3361delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,846 control chromosomes in the GnomAD database, including 2,574 homozygotes. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.18 ( 2574 hom., cov: 28)

Consequence

TILAM
ENST00000509943.2 intron

Scores

Not classified

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.0550

Publications

8 publications found

Variant links:

Genes affected

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

TILAM links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 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
TILAM	ENST00000509943.2 link	n.59+3361delA		intron_variant	Intron 1 of 6	3
TILAM	ENST00000832079.1 link	n.155+2049delA		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27336

AN:

151726

Hom.:

2572

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.00251

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.198

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

GnomAD4 genome

AF:

0.180

AC:

27347

AN:

151846

Hom.:

2574

Cov.:

AF XY:

0.175

AC XY:

12951

AN XY:

74196

show subpopulations

African (AFR)

AF:

0.193

AC:

7988

AN:

41356

American (AMR)

AF:

0.164

AC:

2497

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

701

AN:

3466

East Asian (EAS)

AF:

0.00252

AC:

AN:

5158

South Asian (SAS)

AF:

0.128

AC:

616

AN:

4814

European-Finnish (FIN)

AF:

0.145

AC:

1530

AN:

10550

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.197

AC:

13380

AN:

67916

Other (OTH)

AF:

0.196

AC:

414

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1161

2321

3482

4642

5803

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0595

Hom.:

Bravo

AF:

0.181

Asia WGS

AF:

0.0610

AC:

213

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Bone mineral density variation quantitative trait locus

Other:1

Aug 01, 2009

OMIM

Significance:association

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.055

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

17-50203294-GAA-GA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over