rs9263794

Variant names:

• chr6-31162242-A-G
• rs9263794
• NM_007109.3:c.798-235A>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.798-235A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,106 control chromosomes in the GnomAD database, including 1,802 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 0.15 (1802 hom., cov: 32)
• Consequence: TCF19 NM_007109.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 14 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCF19	NM_007109.3	MANE Select	c.798-235A>G		intron	N/A	NP_009040.2	A0A1U9X8M7
	TCF19	NM_001077511.2		c.798-235A>G		intron	N/A	NP_001070979.1	A0A1U9X8M7
	TCF19	NM_001318908.2		c.798-235A>G		intron	N/A	NP_001305837.1	Q9Y242

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCF19	ENST00000376257.8	TSL:1 MANE Select	c.798-235A>G		intron	N/A	ENSP00000365433.3	Q9Y242
	TCF19	ENST00000376255.4	TSL:1	c.798-235A>G		intron	N/A	ENSP00000365431.4	Q9Y242
	TCF19	ENST00000706778.1		c.798-235A>G		intron	N/A	ENSP00000516543.1	Q9Y242

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22744 AN: 151988 Hom.: 1794 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0925

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.164

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.150 AC: 22789 AN: 152106 Hom.: 1802 Cov.: 32 AF XY: 0.148 AC XY: 10992 AN XY: 74384

African (AFR) AF: 0.164 AC: 6780 AN: 41450

American (AMR) AF: 0.137 AC: 2099 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0925 AC: 321 AN: 3470

East Asian (EAS) AF: 0.0790 AC: 409 AN: 5178

South Asian (SAS) AF: 0.137 AC: 660 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10600

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10803 AN: 67980

Other (OTH) AF: 0.162 AC: 342 AN: 2112

Alfa AF: 0.155 Hom.: 2267

Bravo AF: 0.151

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.78
PhyloP100		-0.061
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: rs9263794; hg19: chr6-31130019;