dbSNP rs3809566: TPM1-AS:n.122+7040T>C (chr15-63041525-A-G) – 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.122+7040T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,124 control chromosomes in the GnomAD database, including 35,600 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 0.68 ( 35600 hom., cov: 33)

Consequence

TPM1-AS
ENST00000804116.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.173

Publications

22 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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.737 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.122+7040T>C		intron_variant	Intron 1 of 3
TPM1-AS	ENST00000804117.1 link	n.171+1863T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.683

AC:

103798

AN:

152006

Hom.:

35564

Cov.:

show subpopulations

Gnomad AFR

AF:

0.691

Gnomad AMI

AF:

0.519

Gnomad AMR

AF:

0.749

Gnomad ASJ

AF:

0.696

Gnomad EAS

AF:

0.556

Gnomad SAS

AF:

0.575

Gnomad FIN

AF:

0.654

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.686

Gnomad OTH

AF:

0.686

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

GnomAD4 genome

AF:

0.683

AC:

103877

AN:

152124

Hom.:

35600

Cov.:

AF XY:

0.679

AC XY:

50517

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.691

AC:

28694

AN:

41514

American (AMR)

AF:

0.749

AC:

11453

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.696

AC:

2414

AN:

3470

East Asian (EAS)

AF:

0.557

AC:

2869

AN:

5154

South Asian (SAS)

AF:

0.574

AC:

2769

AN:

4822

European-Finnish (FIN)

AF:

0.654

AC:

6913

AN:

10576

Middle Eastern (MID)

AF:

0.704

AC:

207

AN:

294

European-Non Finnish (NFE)

AF:

0.686

AC:

46649

AN:

67982

Other (OTH)

AF:

0.682

AC:

1439

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

1723

3446

5170

6893

8616

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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.:

4874

Bravo

AF:

0.692

Asia WGS

AF:

0.556

AC:

1933

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.5

(source)

DANN

Benign

0.70

PhyloP100

-0.17

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