chr6-31163044-C-T

Variant names:

• chr6-31163044-C-T
• rs1044870
• NM_007109.3:c.*327C>T

Variant summary

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

The NM_007109.3(TCF19):​c.*327C>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 0.156 in 1,184,582 control chromosomes in the GnomAD database, including 15,025 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 (1733 hom., cov: 33)
  • Exomes 𝑓: 0.16 (13292 hom.)
• Consequence: TCF19 NM_007109.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 11 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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.*327C>T		3_prime_UTR	Exon 4 of 4	NP_009040.2
	TCF19	NR_199382.1		n.1857C>T		non_coding_transcript_exon	Exon 5 of 5
	TCF19	NM_001077511.2		c.*327C>T		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.*327C>T		3_prime_UTR	Exon 4 of 4	ENSP00000365433.3
	TCF19	ENST00000376255.4	TSL:1	c.*327C>T		3_prime_UTR	Exon 4 of 4	ENSP00000365431.4
	TCF19	ENST00000706785.1		n.*658C>T		non_coding_transcript_exon	Exon 5 of 5	ENSP00000516549.1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22152 AN: 152090 Hom.: 1725 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0920

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.0669

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.158 AC: 162738 AN: 1032374 Hom.: 13292 Cov.: 58 AF XY: 0.157 AC XY: 76164 AN XY: 486340

African (AFR) AF: 0.159 AC: 3638 AN: 22882

American (AMR) AF: 0.116 AC: 1035 AN: 8900

Ashkenazi Jewish (ASJ) AF: 0.0921 AC: 1167 AN: 12674

East Asian (EAS) AF: 0.0370 AC: 763 AN: 20598

South Asian (SAS) AF: 0.0738 AC: 1920 AN: 26020

European-Finnish (FIN) AF: 0.112 AC: 1344 AN: 12034

Middle Eastern (MID) AF: 0.146 AC: 390 AN: 2678

European-Non Finnish (NFE) AF: 0.165 AC: 146670 AN: 886592

Other (OTH) AF: 0.145 AC: 5811 AN: 39996

GnomAD4 genome AF: 0.146 AC: 22197 AN: 152208 Hom.: 1733 Cov.: 33 AF XY: 0.143 AC XY: 10621 AN XY: 74424

African (AFR) AF: 0.160 AC: 6633 AN: 41518

American (AMR) AF: 0.133 AC: 2035 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0920 AC: 319 AN: 3468

East Asian (EAS) AF: 0.0730 AC: 378 AN: 5176

South Asian (SAS) AF: 0.0682 AC: 329 AN: 4822

European-Finnish (FIN) AF: 0.115 AC: 1216 AN: 10602

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10793 AN: 68004

Other (OTH) AF: 0.159 AC: 337 AN: 2114

Alfa AF: 0.153 Hom.: 2045

Bravo AF: 0.147

Asia WGS AF: 0.101 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.4
DANN	Benign	0.76
PhyloP100		0.10
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: rs1044870; hg19: chr6-31130821;