6-31163499-A-T

Position:

• chr6-31163499-A-T

Variant summary

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

The NM_007109.3(TCF19):​c.*782A>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 0.0696 in 985,378 control chromosomes in the GnomAD database, including 2,614 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 (672 hom., cov: 33)
  • Exomes 𝑓: 0.067 (1942 hom.)
• Consequence: TCF19 NM_007109.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCF19	NM_007109.3	c.*782A>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.*782A>T		3_prime_UTR_variant	4/4	1	NM_007109.3	ENSP00000365433.3

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13118 AN: 152144 Hom.: 672 Cov.: 33

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0429

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0665 AC: 55414 AN: 833116 Hom.: 1942 Cov.: 50 AF XY: 0.0663 AC XY: 25506 AN XY: 384720

Gnomad4 AFR exome AF: 0.0561

Gnomad4 AMR exome AF: 0.135

Gnomad4 ASJ exome AF: 0.130

Gnomad4 EAS exome AF: 0.0501

Gnomad4 SAS exome AF: 0.102

Gnomad4 FIN exome AF: 0.174

Gnomad4 NFE exome AF: 0.0651

Gnomad4 OTH exome AF: 0.0740

GnomAD4 genome AF: 0.0862 AC: 13130 AN: 152262 Hom.: 672 Cov.: 33 AF XY: 0.0905 AC XY: 6738 AN XY: 74462

Gnomad4 AFR AF: 0.0549

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0430

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0344 Hom.: 22

Bravo AF: 0.0821

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs17190798; hg19: chr6-31131276;