dbSNP rs2799738: TCEA1P3:n.203A>T (chr9-38478673-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000443005.1(TCEA1P3):n.203A>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.315 in 155,190 control chromosomes in the GnomAD database, including 7,984 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 0.32 ( 7889 hom., cov: 32)

Exomes 𝑓: 0.23 ( 95 hom. )

Consequence

TCEA1P3
ENST00000443005.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.44

Publications

1 publications found

Variant links:

Genes affected

TCEA1P3 (HGNC:30569): (transcription elongation factor A1 pseudogene 3)

TCEA1P3 links:

ENSG00000291061 (HGNC:):

ENSG00000291061 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=-0.59).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCEA1P3		n.38478673A>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TCEA1P3	ENST00000443005.1 link	n.203A>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000291061	ENST00000635962.1 link	n.1044+6740A>T	intron_variant	Intron 8 of 9	5
ENSG00000291061	ENST00000685989.1 link	n.1044+6740A>T	intron_variant	Intron 8 of 10

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48180

AN:

152020

Hom.:

7877

Cov.:

show subpopulations

Gnomad AFR

AF:

0.383

Gnomad AMI

AF:

0.386

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.186

Gnomad SAS

AF:

0.279

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.329

GnomAD4 exome

AF:

0.228

AC:

696

AN:

3052

Hom.:

Cov.:

AF XY:

0.230

AC XY:

372

AN XY:

1616

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.300

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.333

AC:

AN:

132

European-Finnish (FIN)

AF:

0.184

AC:

297

AN:

1610

Middle Eastern (MID)

AF:

0.667

AC:

AN:

European-Non Finnish (NFE)

AF:

0.270

AC:

303

AN:

1124

Other (OTH)

AF:

0.254

AC:

AN:

122

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

111

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.317

AC:

48228

AN:

152138

Hom.:

7889

Cov.:

AF XY:

0.311

AC XY:

23095

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.384

AC:

15907

AN:

41474

American (AMR)

AF:

0.296

AC:

4521

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.365

AC:

1267

AN:

3468

East Asian (EAS)

AF:

0.186

AC:

962

AN:

5172

South Asian (SAS)

AF:

0.278

AC:

1343

AN:

4826

European-Finnish (FIN)

AF:

0.213

AC:

2254

AN:

10580

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.306

AC:

20842

AN:

68002

Other (OTH)

AF:

0.326

AC:

690

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1673

3346

5019

6692

8365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.317

Hom.:

950

Bravo

AF:

0.325

Asia WGS

AF:

0.247

AC:

857

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

5.1

(source)

DANN

Benign

0.56

PhyloP100

6.4

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over