6-31163792-C-T

Position:

• chr6-31163792-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCF19	NM_007109.3	c.*1075C>T		3_prime_UTR_variant	4/4	ENST00000376257.8	NP_009040.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCF19	ENST00000376257.8	c.*1075C>T		3_prime_UTR_variant	4/4	1	NM_007109.3	ENSP00000365433.3

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118674 AN: 152052 Hom.: 46551 Cov.: 33

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.: 42 AF XY: 0.750 AC XY: 288386 AN XY: 384538

Gnomad4 AFR exome AF: 0.857

Gnomad4 AMR exome AF: 0.805

Gnomad4 ASJ exome AF: 0.866

Gnomad4 EAS exome AF: 0.683

Gnomad4 SAS exome AF: 0.724

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.747

Gnomad4 OTH exome AF: 0.764

GnomAD4 genome AF: 0.780 AC: 118767 AN: 152170 Hom.: 46590 Cov.: 33 AF XY: 0.779 AC XY: 57979 AN XY: 74406

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.862

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.816

Alfa AF: 0.771 Hom.: 17845

Bravo AF: 0.790

Asia WGS AF: 0.755 AC: 2626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.33

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

LitVar

Other links and lift over

dbSNP: rs3132528; hg19: chr6-31131569; COSMIC: COSV105012452; COSMIC: COSV105012452;