Genetic Variant NM_007109.3:c.*1075C>T (chr6-31163792-C-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.*1075C>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 0.755 in 984,904 control chromosomes in the GnomAD database, including 280,918 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 0.78 ( 46590 hom., cov: 33)

Exomes 𝑓: 0.75 ( 234328 hom. )

Consequence

TCF19
NM_007109.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

26 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:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 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	UniProt
TCF19	NM_007109.3	MANE Select	c.*1075C>T	3_prime_UTR	Exon 4 of 4	NP_009040.2	A0A1U9X8M7
TCF19	NM_001077511.2		c.*1075C>T	3_prime_UTR	Exon 4 of 4	NP_001070979.1	A0A1U9X8M7
TCF19	NM_001318908.2		c.*1075C>T	3_prime_UTR	Exon 5 of 5	NP_001305837.1	Q9Y242

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TCF19	ENST00000376257.8	TSL:1 MANE Select	c.*1075C>T	3_prime_UTR	Exon 4 of 4	ENSP00000365433.3	Q9Y242
TCF19	ENST00000376255.4	TSL:1	c.*1075C>T	3_prime_UTR	Exon 4 of 4	ENSP00000365431.4	Q9Y242
TCF19	ENST00000706778.1		c.*1075C>T	3_prime_UTR	Exon 5 of 5	ENSP00000516543.1	Q9Y242

Frequencies

GnomAD3 genomes

AF:

0.780

AC:

118674

AN:

152052

Hom.:

46551

Cov.:

show subpopulations

Gnomad AFR

AF:

0.847

Gnomad AMI

AF:

0.806

Gnomad AMR

AF:

0.805

Gnomad ASJ

AF:

0.862

Gnomad EAS

AF:

0.679

Gnomad SAS

AF:

0.688

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.889

Gnomad NFE

AF:

0.747

Gnomad OTH

AF:

0.817

GnomAD4 exome

AF:

0.750

AC:

624448

AN:

832734

Hom.:

234328

Cov.:

AF XY:

0.750

AC XY:

288386

AN XY:

384538

show subpopulations

African (AFR)

AF:

0.857

AC:

13526

AN:

15782

American (AMR)

AF:

0.805

AC:

792

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.866

AC:

4462

AN:

5150

East Asian (EAS)

AF:

0.683

AC:

2474

AN:

3622

South Asian (SAS)

AF:

0.724

AC:

11909

AN:

16452

European-Finnish (FIN)

AF:

0.750

AC:

207

AN:

276

Middle Eastern (MID)

AF:

0.846

AC:

1370

AN:

1620

European-Non Finnish (NFE)

AF:

0.747

AC:

568863

AN:

761564

Other (OTH)

AF:

0.764

AC:

20845

AN:

27284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.419

Heterozygous variant carriers

10184

20369

30553

40738

50922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18970

37940

56910

75880

94850

<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:

0.780

AC:

118767

AN:

152170

Hom.:

46590

Cov.:

AF XY:

0.779

AC XY:

57979

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.847

AC:

35173

AN:

41508

American (AMR)

AF:

0.805

AC:

12296

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.862

AC:

2993

AN:

3472

East Asian (EAS)

AF:

0.679

AC:

3512

AN:

5170

South Asian (SAS)

AF:

0.687

AC:

3318

AN:

4832

European-Finnish (FIN)

AF:

0.749

AC:

7926

AN:

10588

Middle Eastern (MID)

AF:

0.884

AC:

260

AN:

294

European-Non Finnish (NFE)

AF:

0.747

AC:

50828

AN:

67998

Other (OTH)

AF:

0.816

AC:

1726

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1352

2704

4057

5409

6761

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

864

1728

2592

3456

4320

<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:

0.763

Hom.:

92478

Bravo

AF:

0.790

Asia WGS

AF:

0.755

AC:

2626

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.87

(source)

DANN

Benign

0.33

PhyloP100

-1.0

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

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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