6-31163930-T-C

Position:

• chr6-31163930-T-C

Variant summary

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

The NM_007109.3(TCF19):​c.*1213T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 985,596 control chromosomes in the GnomAD database, including 994 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 0.064 (508 hom., cov: 32)
  • Exomes 𝑓: 0.027 (486 hom.)
• Consequence: TCF19 NM_007109.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCF19	NM_007109.3	c.*1213T>C		3_prime_UTR_variant	4/4	ENST00000376257.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCF19	ENST00000376257.8	c.*1213T>C		3_prime_UTR_variant	4/4	1	NM_007109.3	P1

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9696 AN: 151916 Hom.: 506 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0419

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.0636

GnomAD4 exome AF: 0.0271 AC: 22623 AN: 833562 Hom.: 486 Cov.: 32 AF XY: 0.0270 AC XY: 10384 AN XY: 384958

Gnomad4 AFR exome AF: 0.138

Gnomad4 AMR exome AF: 0.0400

Gnomad4 ASJ exome AF: 0.0285

Gnomad4 EAS exome AF: 0.165

Gnomad4 SAS exome AF: 0.0341

Gnomad4 FIN exome AF: 0.0504

Gnomad4 NFE exome AF: 0.0234

Gnomad4 OTH exome AF: 0.0446

GnomAD4 genome AF: 0.0638 AC: 9700 AN: 152034 Hom.: 508 Cov.: 32 AF XY: 0.0651 AC XY: 4837 AN XY: 74328

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0338

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0419

Gnomad4 FIN AF: 0.0528

Gnomad4 NFE AF: 0.0241

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0335 Hom.: 219

Bravo AF: 0.0672

Asia WGS AF: 0.113 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.76

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: rs9501062; hg19: chr6-31131707;