6-31162816-G-A

Variant names:

• chr6-31162816-G-A
• rs1419881
• NM_007109.3:c.*99G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_007109.3(TCF19):​c.*99G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 1,497,584 control chromosomes in the GnomAD database, including 172,104 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 0.50 (19630 hom., cov: 31)
  • Exomes 𝑓: 0.47 (152474 hom.)
• Consequence: TCF19 NM_007109.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94
• Publications: 76 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCF19	NM_007109.3	MANE Select	c.*99G>A		3_prime_UTR	Exon 4 of 4	NP_009040.2
	TCF19	NR_199382.1		n.1629G>A		non_coding_transcript_exon	Exon 5 of 5
	TCF19	NM_001077511.2		c.*99G>A		3_prime_UTR	Exon 4 of 4	NP_001070979.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCF19	ENST00000376257.8	TSL:1 MANE Select	c.*99G>A		3_prime_UTR	Exon 4 of 4	ENSP00000365433.3
	TCF19	ENST00000376255.4	TSL:1	c.*99G>A		3_prime_UTR	Exon 4 of 4	ENSP00000365431.4
	TCF19	ENST00000496421.1	TSL:3	n.689G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76281 AN: 151824 Hom.: 19624 Cov.: 31

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.474 AC: 637600 AN: 1345644 Hom.: 152474 Cov.: 59 AF XY: 0.471 AC XY: 310425 AN XY: 659308

African (AFR) AF: 0.620 AC: 19241 AN: 31048

American (AMR) AF: 0.471 AC: 15094 AN: 32064

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 9160 AN: 21048

East Asian (EAS) AF: 0.545 AC: 20036 AN: 36770

South Asian (SAS) AF: 0.420 AC: 29998 AN: 71354

European-Finnish (FIN) AF: 0.431 AC: 14140 AN: 32842

Middle Eastern (MID) AF: 0.437 AC: 1750 AN: 4002

European-Non Finnish (NFE) AF: 0.473 AC: 501251 AN: 1060402

Other (OTH) AF: 0.480 AC: 26930 AN: 56114

GnomAD4 genome AF: 0.502 AC: 76317 AN: 151940 Hom.: 19630 Cov.: 31 AF XY: 0.498 AC XY: 36992 AN XY: 74264

African (AFR) AF: 0.616 AC: 25506 AN: 41434

American (AMR) AF: 0.487 AC: 7433 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1452 AN: 3464

East Asian (EAS) AF: 0.549 AC: 2834 AN: 5164

South Asian (SAS) AF: 0.416 AC: 1998 AN: 4808

European-Finnish (FIN) AF: 0.414 AC: 4370 AN: 10554

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31147 AN: 67928

Other (OTH) AF: 0.478 AC: 1009 AN: 2110

Alfa AF: 0.475 Hom.: 57712

Bravo AF: 0.515

Asia WGS AF: 0.511 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	23
DANN	Benign	0.82
PhyloP100		2.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.22		Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1419881; hg19: chr6-31130593;