6-31163432-A-G

Variant names:

• chr6-31163432-A-G
• rs17190783
• NM_007109.3:c.*715A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007109.3(TCF19):​c.*715A>G 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 985,412 control chromosomes in the GnomAD database, including 2,613 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 (1941 hom.)
• Consequence: TCF19 NM_007109.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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 rank	MANE	Protein	UniProt
TCF19	NM_007109.3	c.*715A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000376257.8	NP_009040.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCF19	ENST00000376257.8	c.*715A>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_007109.3	ENSP00000365433.3

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13121 AN: 152180 Hom.: 672 Cov.: 33

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0429

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0665 AC: 55407 AN: 833114 Hom.: 1941 Cov.: 46 AF XY: 0.0663 AC XY: 25505 AN XY: 384716

African (AFR) AF: 0.0562 AC: 887 AN: 15786

American (AMR) AF: 0.135 AC: 133 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 670 AN: 5152

East Asian (EAS) AF: 0.0501 AC: 182 AN: 3630

South Asian (SAS) AF: 0.102 AC: 1671 AN: 16460

European-Finnish (FIN) AF: 0.173 AC: 49 AN: 284

Middle Eastern (MID) AF: 0.117 AC: 190 AN: 1620

European-Non Finnish (NFE) AF: 0.0651 AC: 49605 AN: 761896

Other (OTH) AF: 0.0740 AC: 2020 AN: 27302

GnomAD4 genome AF: 0.0862 AC: 13133 AN: 152298 Hom.: 672 Cov.: 33 AF XY: 0.0905 AC XY: 6739 AN XY: 74472

African (AFR) AF: 0.0550 AC: 2285 AN: 41568

American (AMR) AF: 0.118 AC: 1801 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3472

East Asian (EAS) AF: 0.0430 AC: 223 AN: 5192

South Asian (SAS) AF: 0.0943 AC: 455 AN: 4826

European-Finnish (FIN) AF: 0.179 AC: 1903 AN: 10610

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.0818 AC: 5564 AN: 68012

Other (OTH) AF: 0.113 AC: 240 AN: 2116

Alfa AF: 0.0847 Hom.: 137

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	-0.88
CADD	Benign	3.1
DANN	Benign	0.57
PhyloP100		0.058
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17190783; hg19: chr6-31131209; COSMIC: COSV105012435; COSMIC: COSV105012435;