ENST00000412749.2:n.237+3897A>G

Variant names:

• chr2-27361799-A-G
• rs7586601
• ENST00000412749.2:n.237+3897A>G

Variant summary

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

The ENST00000412749.2(GTF3C2-AS2):​n.237+3897A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,914 control chromosomes in the GnomAD database, including 23,351 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 0.53 (23351 hom., cov: 30)
• Consequence: GTF3C2-AS2 ENST00000412749.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 30 publications found

Genes affected

GTF3C2-AS2 (HGNC:55699): (GTF3C2 antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GTF3C2-AS2	NR_183825.1	n.1745+2339A>G		intron_variant	Intron 2 of 2
GTF3C2-AS2	NR_183826.1	n.668+2339A>G		intron_variant	Intron 2 of 2
GTF3C2-AS2	NR_183827.1	n.763+2339A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GTF3C2-AS2	ENST00000412749.2	n.237+3897A>G		intron_variant	Intron 2 of 2	3
GTF3C2-AS2	ENST00000847761.1	n.302+3897A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80153 AN: 151796 Hom.: 23285 Cov.: 30

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.529 AC: 80290 AN: 151914 Hom.: 23351 Cov.: 30 AF XY: 0.523 AC XY: 38855 AN XY: 74240

African (AFR) AF: 0.774 AC: 32082 AN: 41438

American (AMR) AF: 0.521 AC: 7936 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1295 AN: 3468

East Asian (EAS) AF: 0.155 AC: 801 AN: 5182

South Asian (SAS) AF: 0.461 AC: 2223 AN: 4822

European-Finnish (FIN) AF: 0.465 AC: 4905 AN: 10544

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29546 AN: 67920

Other (OTH) AF: 0.474 AC: 1000 AN: 2108

Alfa AF: 0.451 Hom.: 19025

Bravo AF: 0.542

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.81
DANN	Benign	0.71
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7586601; hg19: chr2-27584666;