chr2-27328100-A-T

Variant names:

• chr2-27328100-A-T
• rs1049817
• NM_001035521.3:c.2346T>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001035521.3(GTF3C2):​c.2346T>A​(p.Pro782Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: GTF3C2 NM_001035521.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 44 publications found

Genes affected

GTF3C2 (HGNC:4665): (general transcription factor IIIC subunit 2) Contributes to DNA binding activity. Involved in transcription by RNA polymerase III. Located in nucleoplasm. Part of transcription factor TFIIIC complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.029).
• BP7: Synonymous conserved (PhyloP=-0.246 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001035521.3. 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
	GTF3C2	NM_001035521.3	MANE Select	c.2346T>A	p.Pro782Pro	synonymous	Exon 17 of 19	NP_001030598.1
	GTF3C2	NM_001318909.4		c.2346T>A	p.Pro782Pro	synonymous	Exon 17 of 19	NP_001305838.2
	GTF3C2	NM_001388380.3		c.2346T>A	p.Pro782Pro	synonymous	Exon 18 of 20	NP_001375309.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GTF3C2	ENST00000264720.8	TSL:1 MANE Select	c.2346T>A	p.Pro782Pro	synonymous	Exon 17 of 19	ENSP00000264720.3
	GTF3C2	ENST00000359541.6	TSL:1	c.2346T>A	p.Pro782Pro	synonymous	Exon 17 of 19	ENSP00000352536.2
	GTF3C2	ENST00000454704.5	TSL:1	c.870T>A	p.Pro290Pro	synonymous	Exon 8 of 10	ENSP00000393429.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 57446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	7.6
DANN	Benign	0.82
PhyloP100		-0.25
PromoterAI		-0.0014	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism

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: rs1049817; hg19: chr2-27550967;