dbSNP rs2586502: TILAM:n.131-237C>A (chr17-50211709-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.95

Publications

12 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 -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	Effect	Exon rank	TSL
TILAM	ENST00000509943.2 link	n.131-237C>A	intron_variant	Intron 2 of 6	3
TILAM	ENST00000514468.3 link	n.384+907C>A	intron_variant	Intron 3 of 7	3
TILAM	ENST00000650459.1 link	n.252-2126C>A	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.865

AC:

131422

AN:

152008

Hom.:

57549

Cov.:

show subpopulations

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.:

AF XY:

0.869

AC XY:

64654

AN XY:

74380

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

840

1680

2519

3359

4199

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

886

1772

2658

3544

4430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.11

(source)

DANN

Benign

0.27

PhyloP100

-6.0

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over