Genetic Variant TFAP2A-AS1:n.195+8914G>C (chr6-10420248-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000718199.1(TFAP2A-AS1):n.195+8914G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,122 control chromosomes in the GnomAD database, including 8,669 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 0.23 ( 8669 hom., cov: 33)

Consequence

TFAP2A-AS1
ENST00000718199.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.718

Publications

2 publications found

Variant links:

Genes affected

TFAP2A-AS1 (HGNC:40579): (TFAP2A antisense RNA 1)

TFAP2A-AS1 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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
TFAP2A-AS1	ENST00000718199.1 link	n.195+8914G>C		intron_variant	Intron 1 of 3
TFAP2A-AS1	ENST00000718201.1 link	n.284+4868G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35533

AN:

152004

Hom.:

8644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.618

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.143

Gnomad ASJ

AF:

0.0632

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.0870

Gnomad FIN

AF:

0.0624

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0675

Gnomad OTH

AF:

0.203

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

GnomAD4 genome

AF:

0.234

AC:

35600

AN:

152122

Hom.:

8669

Cov.:

AF XY:

0.228

AC XY:

16983

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.618

AC:

25647

AN:

41506

American (AMR)

AF:

0.142

AC:

2174

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0632

AC:

219

AN:

3464

East Asian (EAS)

AF:

0.275

AC:

1422

AN:

5166

South Asian (SAS)

AF:

0.0862

AC:

416

AN:

4826

European-Finnish (FIN)

AF:

0.0624

AC:

660

AN:

10580

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0675

AC:

4586

AN:

67988

Other (OTH)

AF:

0.200

AC:

421

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

949

1897

2846

3794

4743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

306

612

918

1224

1530

<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:

0.0343

Hom.:

Bravo

AF:

0.259

Asia WGS

AF:

0.189

AC:

660

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.3

(source)

DANN

Benign

0.69

PhyloP100

-0.72

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