Genetic Variant TPM1-AS:n.373+866A>G (chr15-63020496-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000804116.1(TPM1-AS):n.373+866A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,150 control chromosomes in the GnomAD database, including 33,287 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 0.65 ( 33287 hom., cov: 33)

Consequence

TPM1-AS
ENST00000804116.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.903

Publications

3 publications found

Variant links:

Genes affected

TPM1-AS (HGNC:53635): (TPM1 antisense RNA)

TPM1-AS 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=-0.66).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 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
TPM1-AS	ENST00000804116.1 link	n.373+866A>G		intron_variant	Intron 3 of 3
TPM1-AS	ENST00000804117.1 link	n.422+866A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.649

AC:

98706

AN:

152032

Hom.:

33276

Cov.:

show subpopulations

Gnomad AFR

AF:

0.568

Gnomad AMI

AF:

0.859

Gnomad AMR

AF:

0.667

Gnomad ASJ

AF:

0.793

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.481

Gnomad FIN

AF:

0.707

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.725

Gnomad OTH

AF:

0.688

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

GnomAD4 genome

AF:

0.649

AC:

98757

AN:

152150

Hom.:

33287

Cov.:

AF XY:

0.642

AC XY:

47806

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.568

AC:

23570

AN:

41478

American (AMR)

AF:

0.666

AC:

10181

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.793

AC:

2749

AN:

3466

East Asian (EAS)

AF:

0.135

AC:

701

AN:

5180

South Asian (SAS)

AF:

0.481

AC:

2320

AN:

4824

European-Finnish (FIN)

AF:

0.707

AC:

7494

AN:

10596

Middle Eastern (MID)

AF:

0.748

AC:

220

AN:

294

European-Non Finnish (NFE)

AF:

0.725

AC:

49291

AN:

68004

Other (OTH)

AF:

0.684

AC:

1448

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1700

3399

5099

6798

8498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

776

1552

2328

3104

3880

<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:

0.676

Hom.:

4319

Bravo

AF:

0.647

Asia WGS

AF:

0.350

AC:

1222

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

3.1

(source)

DANN

Benign

0.88

PhyloP100

-0.90

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