5-150374331-G-C

Variant names:

• chr5-150374331-G-C
• rs144327167
• NM_001371623.1:c.1028G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001371623.1(TCOF1):​c.1028G>C​(p.Ser343Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000704 in 1,419,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S343N) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.0e-7 (0 hom.)
• Consequence: TCOF1 NM_001371623.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73

Genes affected

TCOF1 (HGNC:11654): (treacle ribosome biogenesis factor 1) This gene encodes a nucleolar protein with a LIS1 homology domain. The protein is involved in ribosomal DNA gene transcription through its interaction with upstream binding factor (UBF). Mutations in this gene have been associated with Treacher Collins syndrome, a disorder which includes abnormal craniofacial development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22797722).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCOF1	NM_001371623.1	c.1028G>C	p.Ser343Thr	missense_variant	Exon 8 of 27	ENST00000643257.2	NP_001358552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCOF1	ENST00000643257.2	c.1028G>C	p.Ser343Thr	missense_variant	Exon 8 of 27		NM_001371623.1	ENSP00000493815.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000554 AC: 1 AN: 180492 Hom.: 0 AF XY: 0.0000104 AC XY: 1 AN XY: 96090

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000372

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 7.04e-7 AC: 1 AN: 1419478 Hom.: 0 Cov.: 32 AF XY: 0.00000142 AC XY: 1 AN XY: 702390

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000262

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	22
DANN	Benign	0.96
DEOGEN2	Benign	0.26	.;T;.;.;.;.;.;.;.;.;T;T
Eigen	Benign	0.12
Eigen_PC	Benign	-0.0028
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Benign	0.53	T;T;T;T;.;T;T;T;T;T;.;T
M_CAP	Benign	0.036	D
MetaRNN	Benign	0.23	T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.62	T
MutationAssessor	Pathogenic	3.1	.;M;.;.;M;.;M;M;M;M;M;.
PrimateAI	Benign	0.40	T
PROVEAN	Uncertain	-2.4	.;N;N;N;.;.;.;N;N;N;N;N
REVEL	Benign	0.21
Sift	Uncertain	0.013	.;D;D;D;.;.;.;D;D;D;D;D
Sift4G	Uncertain	0.026	.;D;T;T;.;.;.;D;T;D;D;D
Polyphen		1.0, 0.97, 0.95	.;D;D;D;.;.;.;P;D;P;D;.
Vest4		0.37, 0.47, 0.48, 0.43, 0.45, 0.42
MutPred		0.26		.;Gain of glycosylation at S342 (P = 0.0701);.;.;Gain of glycosylation at S342 (P = 0.0701);Gain of glycosylation at S342 (P = 0.0701);Gain of glycosylation at S342 (P = 0.0701);Gain of glycosylation at S342 (P = 0.0701);Gain of glycosylation at S342 (P = 0.0701);Gain of glycosylation at S342 (P = 0.0701);Gain of glycosylation at S342 (P = 0.0701);Gain of glycosylation at S342 (P = 0.0701);
MVP		0.67
MPC		0.43
ClinPred		0.73	D
GERP RS		3.0
Varity_R		0.095
gMVP		0.12

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

Publications

LitVar

Other links and lift over

dbSNP: rs144327167; hg19: chr5-149753894;