Genetic Variant TCF19:c.*1343A>T (chr6-31164060-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 NM_007109.3(TCF19):c.*1343A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 1,009,916 control chromosomes in the GnomAD database, including 2,703 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 0.086 ( 676 hom., cov: 32)

Exomes 𝑓: 0.067 ( 2027 hom. )

Consequence

TCF19
NM_007109.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.309

Publications

7 publications found

Variant links:

Genes affected

TCF19 (HGNC:11629): (transcription factor 19) This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

TCF19 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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007109.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TCF19	NM_007109.3	MANE Select	c.*1343A>T	3_prime_UTR	Exon 4 of 4	NP_009040.2
TCF19	NR_199382.1		n.2873A>T	non_coding_transcript_exon	Exon 5 of 5
TCF19	NM_001077511.2		c.*1343A>T	3_prime_UTR	Exon 4 of 4	NP_001070979.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TCF19	ENST00000376257.8	TSL:1 MANE Select	c.*1343A>T	3_prime_UTR	Exon 4 of 4	ENSP00000365433.3
TCF19	ENST00000376255.4	TSL:1	c.*1343A>T	3_prime_UTR	Exon 4 of 4	ENSP00000365431.4
TCF19	ENST00000706785.1		n.*1674A>T	non_coding_transcript_exon	Exon 5 of 5	ENSP00000516549.1

Frequencies

GnomAD3 genomes

AF:

0.0863

AC:

13127

AN:

152150

Hom.:

676

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0550

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.0429

Gnomad SAS

AF:

0.0945

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.0819

Gnomad OTH

AF:

0.112

GnomAD4 exome

AF:

0.0669

AC:

57337

AN:

857648

Hom.:

2027

Cov.:

AF XY:

0.0667

AC XY:

26470

AN XY:

396744

show subpopulations

African (AFR)

AF:

0.0561

AC:

916

AN:

16340

American (AMR)

AF:

0.125

AC:

414

AN:

3306

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

814

AN:

6214

East Asian (EAS)

AF:

0.0470

AC:

339

AN:

7216

South Asian (SAS)

AF:

0.0992

AC:

1756

AN:

17704

European-Finnish (FIN)

AF:

0.152

AC:

AN:

368

Middle Eastern (MID)

AF:

0.118

AC:

205

AN:

1734

European-Non Finnish (NFE)

AF:

0.0653

AC:

50680

AN:

775900

Other (OTH)

AF:

0.0747

AC:

2157

AN:

28866

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

3211

6423

9634

12846

16057

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2628

5256

7884

10512

13140

<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:

0.0863

AC:

13139

AN:

152268

Hom.:

676

Cov.:

AF XY:

0.0906

AC XY:

6747

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0550

AC:

2288

AN:

41564

American (AMR)

AF:

0.118

AC:

1804

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.132

AC:

458

AN:

3470

East Asian (EAS)

AF:

0.0430

AC:

223

AN:

5190

South Asian (SAS)

AF:

0.0946

AC:

456

AN:

4820

European-Finnish (FIN)

AF:

0.179

AC:

1894

AN:

10580

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0819

AC:

5571

AN:

68028

Other (OTH)

AF:

0.113

AC:

239

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

619

1239

1858

2478

3097

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0833

Hom.:

Bravo

AF:

0.0821

Asia WGS

AF:

0.0780

AC:

272

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.7

(source)

DANN

Benign

0.56

PhyloP100

0.31

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over